mikejseo / sam Goto Github PK

install.packages("samr") returns "Warning in install.packages :
package ‘samr’ is not available (for R version 3.4.3)"

Is there a away to get arounds this? Such as downloading samr directly? or do I need to update my version of R (this would make it incompatible with some other programs I have?)

Thanks!

I think that R is trying to compile the package using gfortran, but its looking at the wrong directory. I use a mac and my gcc is from the brew formula gcc which contains gfortan. I fixed this by downloading the gfortran as specified here https://gcc.gnu.org/wiki/GFortranBinaries.

install.packages("samr")
  --- Please select a CRAN mirror for use in this session ---
  Package which is only available in source form, and may need
    compilation of C/C++/Fortran: ‘samr’
  Do you want to attempt to install these from sources?
  y/n: y
  installing the source package ‘samr’
  
  trying URL 'https://cloud.r-project.org/src/contrib/samr_2.0.tar.gz'
  Content type 'application/x-gzip' length 36702 bytes (35 KB)
  ==================================================
  downloaded 35 KB

  * installing *source* package ‘samr’ ...
  ** libs
  gfortran   -fPIC  -g -O2  -c rankcol.f -o rankcol.o
  clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o samr.so rankcol.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
  ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
  ld: library not found for -lgfortran
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  make: *** [samr.so] Error 1
  ERROR: compilation failed for package ‘samr’
  * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/samr’

  The downloaded source packages are in
  	‘/private/var/folders/v_/n5nqr5812074ct0zkldqhg500000gn/T/RtmpBn8P5n/downloaded_packages’
  Warning message:
  In install.packages("samr") :
    installation of package ‘samr’ had non-zero exit status

Hi Mike,

On the start:

library(shiny)
runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz

The following diagnostics pops up:

Listening on http://127.0.0.1:6297
Error in tag("div", list(...)) :
could not find function "shinyFilesButton"
In addition: Warning message:
In mySI2(internet2_start) : internet routines were already initialized
Error in tag("div", list(...)) :
could not find function "shinyFilesButton"

The same error appears in the browser.

Cheers.

Hi,
I've been having trouble saving my results from a two-class unpaired SAM. My screen turns gray and no results are saved to the location I designate.
Any advice?

Hi,
I am using your SAM for DNA methylation HM450 analysis. I am using beta value of 180 tumor and 10 normal sample. When I am running SAM I am getting this warning:

Warning in run(timeoutMs) : value out of range in 'gammafn'

Although I am getting results but I am not sure is this result is correct or not as I am getting this error continuously. Mean time I also try "samr" in R again I am getting this error:

Warning message:
In factorial(length(y)) : value out of range in 'gammafn'

I don't know exactly about this warning, this warning can affect my analysis? How I can overcome with this waning?

Thanks
Nitish

Hello, I am new at SAM and I want to do it on a microarray data. I uploaded my data and clicked run but I have an error as "missing value where TRUE/FALSE needed" and I filled all blanks in expression data as "NA" and missing gene symbols as "EMPTY" or windows suddenly closes with an error I could not read because of it was too quick.
Why my data has this error? How can I fix this?

I uploaded my data to Google Drive. Can someone help me about that? I use RStudio.

https://drive.google.com/open?id=0B_JS-1GnYihbMkdVNUo3a1J2Z0k

Best regards,

SAM and everything opens and uploads Excel file just fine, AND did with MANY excel sheets that look exactly the same but have 3 that come up with this error when saving:

Warning: Error in <-: length of 'dimnames' [2] not equal to array extent
77: samr.compute.siggenes.table
76: reactive:getAllgenesTable [C:\Users\jessmk\AppData\Local\Temp\RtmpMVWhla\shinyapp7b801fa73be9\SAM-d998a4ed8cba4b7f071ec7f3b5b9606f4c192eed/server.R#472]
60: getAllgenesTable
47: observe [C:\Users\jessmk\AppData\Local\Temp\RtmpMVWhla\shinyapp7b801fa73be9\SAM-d998a4ed8cba4b7f071ec7f3b5b9606f4c192eed/server.R#916]
46:
3: runApp
2: runUrl
1: runGitHub

No difference in the files that worked versus those that give this error so unsure of how to go about fixing the issue, everything I have found via google does not work.

I keep getting this message after running my file (attached):

Error: Non-integer values not alled when assay.type='seq'

The input table contains integers, and I have followed the instructions in samr.pdf and sam.pdf manuals for how to format the table. As far as I can tell, my table looks exactly like the Two Class.xlsx example in this repository (except my data are 'Sequencing' not Array type).

Could you please provide an example for how the 'Sequencing' table should be formatted? Is there something wrong with my table or is there a bug?

Thank you.

salmon_counts_est_genes_integer_SAMseq.xlsx

Hellow, Mike,
I ran the SAM
->library(shiny)
->runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz
The web openned. But after I upload the test data and click "run"button, the following message appared:

Listening on http://127.0.0.1:4077
Warning: Error in impute.knn: 没有"impute.knn"这个函数
132: reactive:getData [C:\Users\dabai\AppData\Local\Temp\Rtmp2RXCDe\shinyapp75413eb142a\SAM-master/server.R#40]
116: getData
115: reactive:getSamrObj [C:\Users\dabai\AppData\Local\Temp\Rtmp2RXCDe\shinyapp75413eb142a\SAM-master/server.R#383]
99: getSamrObj
98: renderText [C:\Users\dabai\AppData\Local\Temp\Rtmp2RXCDe\shinyapp75413eb142a\SAM-master/server.R#747]
97: func
84: origRenderFunc
83: output$samPlotText
3: runApp
2: runUrl
1: runGitHub
Warning: Error in impute.knn: 没有"impute.knn"这个函数
172:
Warning: Error in impute.knn: 没有"impute.knn"这个函数
118:

I have run these codes as you advised elsewhere：
->source("http://bioconductor.org/biocLite.R")
->biocLite("impute")

However this problem still existed.
Do you know how to deal with it? Thanks very much for your help!

Hello, I tried to run SAM using mac (OSX Yosemite version 10.10.1). Everything worked find until I reach to this point

library(shiny)
runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz
Error in runUrl(url, subdir = subdir, destdir = destdir, ...) :
Failed to download URL https://github.com/MikeJSeo/SAM/archive/master.tar.gz
In addition: Warning message:
In download.file(url, method = method, ...) :
download had nonzero exit status

not sure what went wrong, can someone please help me?

thanks

Ella

Hi Mike,
I got this error on a machine with ubuntu 14.04 - R 3.0.2 - rstudio 0.99.446

library(shiny)
runGitHub("sam", "MikeJSeo")
Downloading https://github.com/MikeJSeo/sam/archive/master.tar.gz

Listening on http://127.0.0.1:6038
Loading required namespace: rstudioapi
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.14.0 (2015-02-13) successfully loaded. See ?matrixStats for help.
Error in file(filename, "r", encoding = encoding) :
cannot open connection
Warning in run(timeoutMs) :
cannot open file 'GSA.correlate.revised.R': File or directory not found

Library were correctly installed
please note that PAM works fine.
rstudio terminal window gives this message:
"QSslSocket: cannot resolve SSLv2_client_method"

any suggestion?
Thanks
Luca

Can SAM do post hoc test in multiple group analysis?
Tukey or SNK, et al.

hi,
I am new to R and working with samr package.
I am getting this error " can not allocate vector of size 20.3Mb" after running SAM and do not know how to solve it.
I hope anyone can help.
Thanks in advance.

I have tried the latest version of Chrome, Cortana, IE. Newest and older versions of R and RStudio. Nothing seems to work.

Hi Mike,

Sorry to bombard you with questions, hopefully this is the last one for a while.

I've noticed that using GSA's Multiclass analysis, I only get back results where expression (x) is correlated with the response (y) values. In other words, the order of the response {1,2,3,4,...} matters.

This does not contradict the docs in any way (it mentions that positive results are those where higher expression correlates with higher values of the phenotype, etc.), however, I am wondering if there's a way to test the null of any correlation between class and expression (i.e. class order 1,2,3,4,.. is meaningless, and could just as well reflect classes a,b,c,...).

Thanks!
Roy

Hi Mike,

Is there anywhere in SAM package that you'd perform between-sample normalization to account for different sequencing depth variation between samples? In other words, does SAM need un-normalized or normalized counts to perform the significance analysis?

Thank you
Amin

Hello Mike,

it seems the package "samr" is no longer available on Cran. When installing samr i get:

Warning in install.packages :
package ‘samr’ is not available (for R version 3.4.0)

I first thought it was an issue with the Version of R so i tried older or newer versions, however none of them worked. I also tried to download the package from the Cran website. However, it has has been removed. The latest Version in the archive is "samr_2.0.tar.gz" so i downloaded this. When i tried to install it however, i get the the Error:

• installing source package 'samr' ...
  ** libs

*** arch - i386
Warnung: Ausführung von Kommando 'make -f "D:/Programs/R-3.4.0/etc/i386/Makeconf" -f "D:/Programs/R-3.4.0/share/make/winshlib.mk" SHLIB="samr.dll" SHLIB_LIBADD='$(FLIBS)' OBJECTS="rankcol.o"' ergab Status 127
ERROR: compilation failed for package 'samr'

• removing 'D:/Programs/R-3.4.0/library/samr'
  Warning in install.packages :
  running command '"D:/Programs/R-3.4.0/bin/x64/R" CMD INSTALL -l "D:\Programs\R-3.4.0\library" "C:/Users/Lukas/Downloads/samr_2.0.tar.gz"' had status 1
  Warning in install.packages :
  installation of package ‘C:/Users/Lukas/Downloads/samr_2.0.tar.gz’ had non-zero exit status

I hope you can help me as i am new to R and SAM

Best regards,
Lukas

After a year of using, I now having trouble running the SAM interface. I am getting the following error on R:

install_github("cran/samr")
Downloading GitHub repo cran/samr@master
Skipping 1 packages ahead of CRAN: impute
─ building ‘samr_3.0.tar.gz’information ...v/kj_8j_8j4yncq2kqc1q4mj8w0000gn/T/RtmpqUcnTu/remotes168f5ad02e0d/cran-samr-bf0d63f/DESCRIPTION’ ...

• installing source package ‘samr’ ...
  ** using staged installation
  ** libs
  gfortran -fPIC -Wall -g -O2 -c rankcol.f -o rankcol.o
  make: gfortran: No such file or directory
  make: *** [rankcol.o] Error 1
  ERROR: compilation failed for package ‘samr’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/samr’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/samr’
  Error: Failed to install 'samr' from GitHub:
  (converted from warning) installation of package ‘/var/folders/cv/kj_8j_8j4yncq2kqc1q4mj8w0000gn/T//RtmpqUcnTu/file168f4e0b7335/samr_3.0.tar.gz’

When I open the SAM interface (# runGitHub("SAM", "MikeJSeo")) and upload data that I have analyzed before, I am now getting the following error:

DataTables warning: table id=DataTables_Table_0 - Requested unknown parameter '5' for row 0. For more information about this error, please see http://datatables.net/tn/4

Hi, Mike

I am encountering following error while running a shiny app using r studio:
"function 'Rcpp_precious_remove' not provided by package 'Rcpp"

Hello, I tried to do GSA but it showed "Error in =: number of items to replace is not a multiple of replacement length " in the R interface. What should I do to solve this problem. Many thanks.

I am seeking to run SAM on an xlsx file. There are no missing values and data is in the correct format as I have run SAM previously on an xlsx file formatted the exact same way.

Can you provide any insight as to why this is happening?

Thank you,
David Paulucci

Hi Mike. Been running SAM for years as an Excel addin, but with minimal-to-no expertise in R or the new SAM. (Just loaded it to make SAM work). On a new Windows 10 PC I newly loaded R 3.4.3 and tried to run the code as noted in the README. It seemed to successfully install the packages, and when I ran the next bit:
library(shiny)
runGitHub("SAM", "MikeJSeo")

It opened a Chrome window with the app, although everything is rather dark grey.(... supposed to be)?
I browsed for the xlsx spreadsheet (one I've used in SAM before) and picked the proper response type and hit Run. Nothing appeared on the screen or changed to suggest that it was running now. After 5-10 min still nothing had changed on the Chrome page screen.

After a short bit, this appeared in the R console window:
Listening on http://127.0.0.1:6779
Warning: Error in : package ‘impute’ required by ‘samr’ could not be found
Stack trace (innermost first):
43: .getRequiredPackages2
42: library
3: runApp
2: runUrl
1: runGitHub
Error : package ‘impute’ required by ‘samr’ could not be found

I was unable to close R console or make anything happen using the menus. Finally had to shut it down using Task Manager. Any idea what's going on?
Thanks much!

Hello. I have used the SAM interface to analyse array results. Unfortunately when I try to save my results the screen goes grey and no file is saved. Please could you let me know how I can save my results?

Thanks

Clara

runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz

Listening on http://127.0.0.1:7312
Error in source(file, ..., keep.source = TRUE, encoding = checkEncoding(file)) :
/private/var/folders/2p/69t41kfd1jj9wk93xh4dt3nh0000gn/T/RtmpuzsW5f/shinyapp11e23515976b/SAM-master/server.R:16:1: unexpected input
15:
16: <<

I am current using the two class unpaired shiny SAM (Data type : Array) to analyze variant proportion (Genomic) data. This data ranges from 0-1 and mainly consists of 0s and 1s and numeric values such as 0.67232, etc.

Example data is under:
| | | 1 | 1 | 2 | 2 | 1 |
|chrA;XXXXXXXXX;XXXXXXXXX;G;A | ABC | 1 | 1 | 0 | 0 | 0 |
|chrB;XXXXXXXXX;XXXXXXXXX;G;T | ZYA | 1 | 1 | 0 | 1 | 0.562193 |
| chrC;XXXXXXXX;XXXXXXXX;T;G | ABC1 | 0.9782 | 0 | 1 | 1 | 1 |
|chrD;XXXXXXXX;XXXXXXXX;G;T | LOG1 | 0 | 0 | 1 | 0 | 1 |

When using the same requirement of data input as mentioned in the manual, the program gives me the following error:

Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz

Warning in init.fit$sd < s0 :
  longer object length is not a multiple of shorter object length
Warning in sd + s0 :
  longer object length is not a multiple of shorter object length
perm= 1
Warning in sd + s0 :
  longer object length is not a multiple of shorter object length
perm= 2
Warning in sd + s0 :
  longer object length is not a multiple of shorter object length
…

perm= 100
Warning in sd + s0 :
  longer object length is not a multiple of shorter object length
Warning: Error in <-: replacement has length zero
Stack trace (innermost first):
    94: samr
    93: <reactive:getSamrObj> [C:\Users\MRUPJI\AppData\Local\Temp\RtmpOSzhct\shinyapp1efc1787260c\SAM-master/server.R#398]
    82: getSamrObj
    81: renderText [C:\Users\MRUPJI\AppData\Local\Temp\RtmpOSzhct\shinyapp1efc1787260c\SAM-master/server.R#751]
    80: func
    79: origRenderFunc
    78: output$samPlotText
     3: runApp
     2: runUrl
     1: runGitHub
Warning: Error in <-: replacement has length zero
Stack trace (innermost first):
    104: <Anonymous>
    103: stop
    102: getSamrObj
    101: renderPlot [C:\Users\MRUPJI\AppData\Local\Temp\RtmpOSzhct\shinyapp1efc1787260c\SAM-master/server.R#847]
     91: <reactive:plotObj>
     80: plotObj
     79: origRenderFunc
     78: output$samrPlot
      3: runApp
      2: runUrl
      1: runGitHub
Warning: Error in <-: replacement has length zero
Stack trace (innermost first):
    96: <Anonymous>
    95: stop
    94: getSamrObj
    93: <reactive:getDeltaTable> [C:\Users\MRUPJI\AppData\Local\Temp\RtmpOSzhct\shinyapp1efc1787260c\SAM-master/server.R#405]
    82: getDeltaTable
    81: renderUI [C:\Users\MRUPJI\AppData\Local\Temp\RtmpOSzhct\shinyapp1efc1787260c\SAM-master/server.R#671]
    80: func
    79: origRenderFunc
    78: output$slider
     3: runApp
     2: runUrl
     1: runGitHub

I tried concatenating the first two columns as a single column, to leave the second column blank. In this instance, the third column (with sample data) is treated as the second geneid column and I get an incorrectly calculated output with one missing sample.

| | | 1 | 1 | 2 | 2 | 1 |
|chrA;XXXXXXXXX;XXXXXXXXX;G;A>ABC | | 1 | 1 | 0| 0 | 0 |
|chrB;XXXXXXXXX;XXXXXXXXX;G;T>ZYA | | 1 | 1 |0 |1 |0.562193 |
| chrC;XXXXXXXX;XXXXXXXX;T;G>ABC1 | |0.9782 | 0 | 1 | 1 | 1 |
|chrD;XXXXXXXX;XXXXXXXX;G;T>LOG1 | | 0 | 0 | 1 | 0 | 1 |

Could this be an issue with

1. The abundance of 0s and 1s in the variant data. Which is not very typical of array data?
2. The way the data in read into the program?
3. The presence of unequal number of samples in each group. Eg. 1 has 10 samples and 2 has only 9?

Any help would be greatly appreciated.

Hi Mike and everyone,

I've done multiclass GSA on array data type for 4 classes. I have a couple of questions:

1. In terms of the results, I'm getting a list of positive gene sets only (please see the attachment). I realize that this is normal for multiclass response variable. I wonder though if (like "contrast" for each gene in multiclass gene analysis) it is somehow possible to get a "contrast" for each gene set as well. Because otherwise it's not intuitive how to determine which gene set is enriched in each one of 4 classes.

2. I'm unable to save output into a file because I'm getting an error about argument of length zero. Please see the attachment. I'm not getting this error for multiclass gene analysis done for this dataset and results are saved fine.

Dataset is also attached.

Thanks for your help,
Viktor

4groups_SAM_GSA.xlsx

Hi
i have done the analysis successfully using t-Statistics with two class unpaired response and was able to save the output file. but when i am trying the same analysis with wilcoxon test statistic the permutations are running very slow and showing the significant genes, but when i try to save the output it is crashing with the following error message in R
Computing delta table
1
Warning: Unhandled error in observer: need finite 'ylim' values
observe({
if (input$saveButton != 0) {
isolate({
dir = input$dir
file = input$fname
siggenes.table = getSiggenesTable()
missrate.table = getMissRateTable()
delta.table = getDeltaTable()
samr.assess.samplesize.obj = getSampleSize()
Allgenes = getAllgenesTable()
samr.obj = getSamrObj()
delta = findDelta()
min.foldchange = input$min.foldchange
inputParameters = getInputParameters()
computedValues = getComputedValues()
eigengene = getEigengene()
imputedX = getImputedX()
originalX = getOriginalX()
titleStyle = createStyle(fontSize = 14, fontColour = "#FFFFFF",
halign = "center", fgFill = "#4F81BD")
wb = createWorkbook()
if (!is.null(samr.obj)) {
png(file = "SAMPlot.png")
[... truncated]

If I understood correctly, for quantitative y variables you are using a regression approach. When reading the manual (http://statweb.stanford.edu/~tibs/SAM/sam.pdf) I recognized you said: r_i is the linear regression coefficient of gene i on the outcome". However, the formula given for r_i is not the same as what is written in the code, which is:
r_i = Sum_j x_ij(y_j - mean(y)) / ....
(if I am getting it correctly).
I am also wondering why there is no mean(x_i) in the formula as there normally is in simple linear regression. Any help for me to find the answer is welcome.

Best Regards

Manuel

Hello,

I tried to use your data example in github (Two Class.xlsx) for two class comparison.
But there was error , Javascript Alert "DataTables warning: table ID=DataTables_Table_0- requested unknown parameter '3' for row 0. For more.....'.

Thank you.

Hellow,
When I use an automatic method for S0, how can I get the exact final value (2 or 0.1 or other) which SAM had calculated ?
Thank you very much!

Hi,
I am writing to seek your help in running SAMseq for time course analysis of bulk RNA-seq data. I am interested in using a non-parametric method to

1. find significantly differentially expressed genes that change over time for each protocol, and
2. find differences at specific timepoint between two protocols.

The code I am running below is resulting in an error:

data=list(x=as.matrix(round(samr.norm.data(counts))),y=y, geneid=as.character(1:nrow(counts)), genenames=row.names(counts), logged2=FALSE)
samr.obj<- samr(data, resp.type="One class timecourse", nperms=100, time.summary.type="slope",assay.type='seq')
Estimating sequencing depths...
Resampling to get new data matrices...
12345678
Warning: only one timecourse in one or more classes;
SAM plot and FDRs will be unreliable; only gene scores are informative
Error in if (sum(y == 1) != length(y)) { :
  missing value where TRUE/FALSE needed

I would really appreciate it if you could help me with this error, and point me to the most recent link for the documentation, and if you have any suggestions on other tools that I could use for this analysis.

Thanks in advance for your help.

library(shiny)
runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz

Listening on http://127.0.0.1:3423
Error in source(file, ..., keep.source = TRUE, encoding = checkEncoding(file)) :
C:\Users\AppData\Local\Temp\RtmpegqnJG\shinyapp13803b113541\SAM-master/server.R:16:1: unexpected input
15:
16: <<
^
In addition: Warning message:
In utils::download.file(url, ...) :
downloaded length 1461120 != reported length 200

Hello.

After years of using, I am now having trouble running SAM on MAC OSX 10.13.3 (High Sierra) and R version 3.4.3. I get the following error message:

Listening on http://127.0.0.1:3388
Warning: Error in library: there is no package called ‘samr’
Stack trace (innermost first):
42: library
3: runApp
2: runUrl
1: runGitHub
Error in library(samr) : there is no package called ‘samr’
ERROR: [on_request_read] connection reset by peer

This error seems to be connected to the changes in version number of my MAC OS rather than errors in SAM. Can you please help me?

Thank you for this new SAM interface. I'm having issue after running SAM and exporting the results. The Excel file is damaged and can't be opened. What can I do to solve this problem?

When I upload my .xlsx file I get an error invalid 'description' argument. Any help regarding same will be helpful.

Hi,
I am a beginner and want to analyze my differentially expressed gene.
So, could you please guide me whether I can upload log scale intensity for analysis in SAM. For my log scale probe/gene intensities; Should I run only those genes/probes to check differential expression that has more than 0.5 interquartile or should I run all probes/genes. If I cannot use log value then what statistics should I follow in selecting the probes/genes in linear scale intensities?

Hi
a new issue is appearing while running SAM:

Error in source(file, ..., keep.source = TRUE, encoding = checkEncoding(file)) :
/private/var/folders/5k/lbj04hqn5vqdbtpr4dn950rw0000gn/T/RtmpHBlVWj/shinyapp17a256be05b2/SAM-master/server.R:16:1: unexpected input
15:
16: <<
^

I guess that something went wrong with some updates (I see changes dated "8 hours ago")
Thanks

Hi,

I have a computer where when we Run SAM, it opens in the browser as norma. For some reason, when we click on "select a file" the window that pops up is blank (and on the other machines we can see the local files). We uninstalled R and installed the latest version and reinstalled the packages.

Anything we should be looking for on the computer that is preventing us from browsing our local files not his particular machine?

Thanks!

Hi,I am a college student.I have the following problem.And I don't know how to solve it yet.
I hope you can be helpful.

Unhandled error in observer: zipping up workbook failed. Please make sure Rtools is installed or a zip application is available to R.
Try installr::install.rtools() on Windows.
observe({
if (input$saveButton != 0) {
isolate({
dir = input$dir
file = input$fname
siggenes.table = getSiggenesTable()
missrate.table = getMissRateTable()
delta.table = getDeltaTable()
samr.assess.samplesize.obj = getSampleSize()
Allgenes = getAllgenesTable()
samr.obj = getSamrObj()
delta = findDelta()
min.foldchange = input$min.foldchange
inputParameters = getInputParameters()
computedValues = getComputedValues()
eigengene = getEigengene()
imputedX = getImputedX()
originalX = getOriginalX()
titleStyle = createStyle(fontSize = 14, fontColour = "#FFFFFF",
halign = "center", fgFill = "#4 [... truncated]

Hello,
I am trying to carry out a two class unpaired through the shiny app following runSAM().
When using the example data or my own data in the same format, I am unable to see significant genes as a DataTables warning appears as it seems unable to retrieve the gene names/IDs?

I tried to carry it out on R studio, however couldnt get past creating a samr.obj, with errors 'Error in x[, y == 1, drop = F] : (subscript) logical subscript too long'.

I would greatly appreciate your help, as I am relatively new to R I am probably missing something.

Thank you!

I am encountering following error while running a shiny app using r studio:
"Error in library(dqshiny) : there is no package called ‘dqshiny’"
I installed the package directly from the tools section as well. Still the issue isn't resolved.

Greetings!

I was wondering if it might be possible to modify samr() to be computed in a parallelized manner?

With the current single processor code, running on a large-ish (~50,000 x 750) dataset takes quite a long time, even on a modern machine (going on 3 days now for a survival model via SAMseq()..)

At a glance (I haven't done any profiling..), it seems like there are a few for-loops in the code for samr() that could be parallelized using something like foreach.

Is this something that has been considered?

I load SAM according to your instructions and the SAM window opens up in a new window. I am using RStudio and R 3.2.2.

If I enter the commands here is what happens:

library(shiny)
library(shinyFiles)
runGitHub("SAM", "MikeJSeo")
Downloading https://github.com/MikeJSeo/SAM/archive/master.tar.gz

Listening on http://127.0.0.1:7349
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.14.2 (2015-06-23) successfully loaded. See ?matrixStats for help.
Error in system("wmic logicaldisk get Caption", intern = T) :
'wmic' not found

Not sure what's going on but I can't load any files and therefore can't run the program.

The Code:
deltaTableTwoClass <- samr.compute.delta.table(samrTwoClass,
min.foldchange = 0,
dels = NULL,
nvals = 50)

generates the error:
Error in if (samr.obj$assay.type == "array") { :
argument is of length zero

The samr.obj samrTwoClass seem to be generated correctly by running SAM()

I have a question about the correct input for SAMseq - should it be the matrix of raw read counts (not normalized in any way, e.g.TPM)? I suppose the initial "estimating sequencing depths" step in SAMseq does the normalization, is that correct?
Thank you,
Joanna

Hi, I am trying to use SAM on a Mac M1 R version 4.2.3

This is the code I am running:
sam <- SAM(t(xall),yall,genenames = filteredMZ, geneid = filteredMZ, fdr.output = 0.01, random.seed=2019)
But I get the error:
Error in if (assay.type == "seq" & cond) { : the condition has length > 1
Any help would be appreciated, thanks!

Hi SAM developers,

Running GSA using the R package (GSA, v1.03) I came across an issue related to missing (NA) values.

For a minimal example of this, see the "dummy" example from the PDF docs (here, bottom of page 4 & top of page 5). As it is the example works fine, however, introducing a single NA in the expression matrix, as in x[2,2] <- NA causes the GSA() command to fail with:

Error in rowMeans(x) : 'x' must be an array of at least two dimensions

Am I missing something basic? Or perhaps this is a version issue?

Thanks for your help!

All the best,
Roy

Hi Mike,

I am using MAC with High Sierra to run the RStudio 1.0.143. I got the error information showing "‘shiny’ had non-zero exit status". Then, I use tool to manually install the "shiny". It showed a 2.2MB file been download but still the "non-zero exit status" appeared again. When I library(shiny), it showed "no package called ‘shiny’".

What should I do? Thank you so much.
Best regards,
Joanne

step(1)-------------------------------------------------------------------
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2018c.1.0/zoneinfo/Europe/Zurich'
ERROR: dependency ‘promises’ is not available for package ‘shiny’

• removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/shiny’
  Warning in install.packages :
  installation of package ‘shiny’ had non-zero exit status
  step(2)-------------------------------------------------------------------
  installing the source package ‘shiny’
  trying URL 'https://cran.rstudio.com/src/contrib/shiny_1.1.0.tar.gz'
  Content type 'application/x-gzip' length 2350156 bytes (2.2 MB)
  ==================================================
  downloaded 2.2 MB
  step(3)--------------------------------------------------------------------

library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
runGitHub("SAM", "MikeJSeo")
Error: could not find function "runGitHub"

I'm new to R and i have no idea how to go about it. Please help!

Hi!
When I start SAM i.e. write
runGitHub("SAM", "MikeJSeo")

I get the error-message
Listening on http://127.0.0.1:3095
ERROR: [on_request_read] connection reset by peer

SAM seems to opens in Chrome but I cannot find or open any files for analysis. There does not seem to be any connection.

Any idea what is going on?
SAMR worked on my computer 6 month ago.
Ingrid