I am trying to perform differential analysis on my HT-seq-counts .txt files, using a command below's command,
sampleFiles <- grep("CD39",list.files(directory),value=TRUE) sampleCondition <- sub("(.*annotated...).*","",sampleFiles) sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition) ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)
But I received the error below:
Error in validObject(.Object) : invalid class “DESeqDataSet” object: levels of factors in the design have non-unique level names after make.names() is applied. best to only uobject letters and numbers for levels of factors in the design
Can someone enlighten me please?
My output for sample
My output for
sampleTable is this:
sampleName fileName condition 1 annotated_SRR7059136_CD39-.txt annotated_SRR7059136_CD39-.txt CD39- 2 annotated_SRR7059137_CD39+.txt annotated_SRR7059137_CD39+.txt CD39+ 3 annotated_SRR7059138_CD39-.txt annotated_SRR7059138_CD39-.txt CD39- 4 annotated_SRR7059139_CD39+.txt annotated_SRR7059139_CD39+.txt CD39+ 5 annotated_SRR7059140_CD39-.txt annotated_SRR7059140_CD39-.txt CD39- 6 annotated_SRR7059141_CD39+.txt annotated_SRR7059141_CD39+.txt CD39+ 7 annotated_SRR7059142_CD39-.txt annotated_SRR7059142_CD39-.txt CD39- 8 annotated_SRR7059143_CD39+.txt annotated_SRR7059143_CD39+.txt CD39+
Please advise, thank you!