error running Limma

1

Hi,

I am very new using Galaxy and I am trying to run Limma tools.
I have a rawcountfile with geneID in the first column and the my samples in the other columns. I also have a metadatafile with my sample name and treatment groups.

Both file were successfully loaded but when I run the tool Limma I encountered some errors.

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in .rowNamesDF<-(x, value = value) :
duplicate ‘row.names’ are not allowed
Calls: row.names<- → row.names<-.data.frame → .rowNamesDF<-
Warning message:
non-unique values when setting ‘row.names’: ‘ABCF2’, ‘AHRR’, ‘ARMCX5-GPRASP2’, ‘ATF7’, ‘ATXN7’, ‘CCDC39’, ‘DIABLO’, ‘DUXAP8’, ‘GGT1’, ‘GOLGA8M’, ‘HSPA14’, ‘IGF2’, ‘ITFG2-AS1’, ‘LINC01238’, ‘LINC01505’, ‘LINC02203’, ‘MATR3’, ‘PDE11A’, ‘PINX1’, ‘POLR2J3’, ‘POLR2J4’, ‘PRSS50’, ‘RF00001’, ‘RF00002’, ‘RF00003’, ‘RF00004’, ‘RF00006’, ‘RF00012’, ‘RF00015’, ‘RF00017’, ‘RF00019’, ‘RF00026’, ‘RF00045’, ‘RF00056’, ‘RF00066’, ‘RF00072’, ‘RF00090’, ‘RF00091’, ‘RF00092’, ‘RF00093’, ‘RF00096’, ‘RF00100’, ‘RF00105’, ‘RF00108’, ‘RF00136’, ‘RF00139’, ‘RF00150’, ‘RF00154’, ‘RF00156’, ‘RF00157’, ‘RF00181’, ‘RF00190’, ‘RF00191’, ‘RF00212’, ‘RF00218’, ‘RF00263’, ‘RF00264’, ‘RF00271’, ‘RF00272’, ‘RF00273’, ‘RF00275’, ‘RF00278’, ‘RF00279’, ‘RF00283’, ‘RF00284’, ‘RF00285’, ‘RF00322’, ‘RF00324’, ‘RF00334’, ‘RF00340’, ‘RF00393’, ‘RF00394’, ‘RF00401’, ‘RF00402’, ‘RF00406’, ‘RF00407’, ‘RF00408’, ‘RF00409’, ‘RF00410’, ‘RF00411’, ‘RF00413’, ‘RF00416’, ‘RF00421’, ‘RF00422’, ‘RF00424’, ‘RF00425’, ‘RF00426’, ‘RF00432’, [… truncated]

I have checked that I do not have duplicates so I am confused about the last error.

Thank you for your help,

Charlotte

1 Like
2

Hi @charlottedeg

We also discussed this via email but I am posting back the generalized help here to help future-other-people.

For errors similar to:

duplicate ‘row.names’ are not allowed

The problem is most likely with the version number at the end of some of the gene IDs.

Bioconductor tools sometimes think these are all the same, so it reports “duplicates” when building up the related data matrix.

123456
123456.2 
123456.3

Try reformatting. Watch out for cases where removing the version would actually create a duplicate. You could also do something like: replace the dot with a ZZZ, process the data, then convert ZZZ back to a dot for any downstream graphics or data links.

Since you were using a matrix, this involves a change to just one file. For others a reading: you must make changes to all files that reference those same values.

Related details:

Thanks for reporting the problem, and hope this helps!