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omnideconv / immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods
https://omnideconv.org/immunedeconv/index.html
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Immunedeconv terminates for (non-)duplicate gene symbols #170

Open suhuanhou opened 5 months ago

suhuanhou commented 5 months ago

The error message says:

Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed Calls: ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- In addition: Warning message: non-unique value when setting 'row.names': ‘entry withdrawn’ Execution halted

However, I have double checked the input dataframes. There are no duplicates concerning the HUGO gene symbols in the input data. I also tried converting the HUGO symbols to ENSEMBL, removing duplicate entries again and back transforming it to HUGO symbols (see https://bioinformatics.stackexchange.com/questions/19584/error-of-duplicated-rownames-although-there-are-no-duplicates for explanation). However, I still get the same error for many samples.

I have attached a tar.gz file with two dataframes as examples. One dataframe works (="df_working.Rda") while the other does not (="df_not_working.Rda) with quantiseq.

I would be glad if you could have a look at these files and check what is going wrong with them.

suhuanhou commented 5 months ago

I tried to install version 2.1.3, but it was still version 2.1.0 and the bug was still not fixed.

LorenzoMerotto commented 5 months ago

Hello @suhuanhou I've seen that the version number in the description file of the package was not updated. Nevertheless, it should still be the right version. We were well aware of that bug, but it has not been fixed. You can check #146, specifically this answer, and see if the suggested solution works

joan-yanqiong commented 1 week ago

I installed "omnideconv/immunedeconv@v2.1.0", which seems to work for me.