Question - adding condition to bottom-up data results in NA column about protti

[dschust-r]

Hi Bryan,

Thank you for your question! Could you maybe provide me with more information on what your data frames (both the pd_prot_long and the annotation df) look like exactly (column names and information contained in your columns)? This would really help me to see where the issue might be.

In theory, the joining should work if both data frames (i.e. the one you want to merge with the annotation and the annotation data frame) contain exactly the same file names in a column called "file_name" in both data frames.

Just an example:

# create example data frame with abundances and file names

abundance <- c(1,2,3,1,3,7)

file_name <- c(
  "sample1",
  "sample2",
  "sample3",
  "sample4",
  "sample5",
  "sample6"
)

data <- data.frame(file_name, abundance)

# create annotation data frame

condition <- c(
  "control",
  "control",
  "control",
  "treated",
  "treated",
  "treated"
)
annotation <- data.frame(file_name, condition)

# join both data frames

data_annotated <- data %>%
  left_join(annotation, by = "file_name")

data_annotated will then look like this:

view(data_annotated)

> data_annotated
  file_name abundance condition
1   sample1         1   control
2   sample2         2   control
3   sample3         3   control
4   sample4         1   treated
5   sample5         3   treated
6   sample6         7   treated

All the best,
Dina

[dschust-r]

I just had another look at your file_name vector that you use to make the annotation data frame. To me it looks like your file names in your annotation data frame and pd_prot_long do not match exactly.

E.g. in pd_prot_long your first file name is "abundances_normalized_dmso_1" whereas in your annotation data frame this is "Abundances Normalized DMSO 1".

If you change it to snake case ("abundances_normalized_dmso_1") in your annotation data frame this should work.

Please let me know if that helped you fix the issue.

All the best,
Dina

[bmroger2]

Dina,

You're absolutely correct and I am embarrassed. This code works perfectly fine!

Thank you for the help and for designing such an easy to follow vignette for beginners in R!

Kind regards,
Bryan