pcheng84 / tcgabrowser Goto Github PK

Hi,
Unfortunately, this package is not working properly, especially the first part to get the primary samples. Do you know any replacement for it?

> genome(lusc[[2]]) <- vapply(genome(lusc[[2]]), translateBuild, character(1L))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'genome': subscript is out of bounds
> tnmae <- splitAssays(lusc, c("01", "11"))
Error in splitAssays(lusc, c("01", "11")) : 
  is.list(hitList) || is(hitList, "List") is not TRUE

Kind Regards,
Rahel

Collapse 450k methylation data to gene level

I received the follow error. Any help would be greatly appreciated!

Error: package or namespace load failed for ‘TCGAbrowser’ in namespaceExport(ns, exports):
undefined exports: genecoxsurv, rnamethdeg
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/TCGAbrowser’
  Installation failed: Command failed (1)

Dear Pil Cheng,
I am running TCGAbrowser. I have this error on the pathway analysis. I did the analysis last month without any error on the same same gene set and disease without any error. Can you please help me here:
require(GSVAdata)
data(c2BroadSets)

gene <- "SOX10"
SOX10.pat <- rnasubset(pat, rna, gene, 20)
SOX10.gsva <- rnagsva(SOX10.pat, rna)
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
In addition: Warning messages:
1: In .local(expr, gset.idx.list, ...) :
383genes with constant expression values throuhgout the samples.
2: In .local(expr, gset.idx.list, ...) :
Since argument method!="ssgsea", genes with constant expression values are discarded.
Many thanks in advance,
Rahel

If no differential expressed genes, return "No differentially expressed genes between two groups"

Dear @pcheng84 ,
I have some question regarding rnadeg function that uses voom to produce differentially expressed genes between the high gene and low gene expression groups.

• Are the low gene expression groups the base group for comparison (high VS low exp. groups; that says down-regulated genes are down in high group and up in low exp. group)?
• Is it possible to increase the number of genes in heatmap from top 100 DEGs to more or I have to do it separately in ComplexHeatmap if I want to see top 200 DEGs?
• The last question is that is it possible to include for example two gene of interest to the package workflow for example (SOX10+NRAS) or for this also I should extract the low and high groups separately and make a new pat file myself?

Many thanks in advance, if you could help me in any of those questions!
Kind Regards,
Rahel

check for differential genes, otherwise return a message