Hi everyone, I'm quite new to coding and processing data with the DESeq package, but it seems I will need to use this one for my project. I have a dataset with 14coloms of expression data where I have the names of the genes (row names) in the first col. ( there are about 1400 genes)
The problem is that when I try to use DESeqDataSetFromMatrix I get an error. In case I set up rownames in my df the error is : "Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'ncol': non-numeric variable(s) in data frame: X"
This is because I have the names of the genes that are obviously not numeric. (e.g., KANK1, HTT...etc.)
If I don't set up the row names, I will get an error that says:
.rowNamesDF<-(x, value = value) :
duplicate 'row. names' are not allowed
In addition: Warning message:
non-unique values when setting 'row. names': ‘0’, ‘16’, ‘17’, ‘18’, ‘19’, ‘20’, ‘21’, ‘22’, ‘23’, ‘24’, ‘25’, ‘26’, ‘27’, ‘28’"
So basically, it tries to set up the first column with values in it as row names, and surely there are repetitions bc the expression values might be the same for some genes...
(I also needed to round the data; otherwise, I got an error about integers)
dds <- DESeqDataSetFromMatrix(countData=round(countData), colData=metaData, design=~dex, tidy = TRUE)
Can you recommend something about how to solve my problem? I really appreciate any help you can provide. Thank you, Dorina