i am working in RNA-seq dataset in gastric cancer. i am doing differential expression using DeSeq2 in usegalaxy. While doing i am getting this error
how can i solve this issue? Please help.
do you by any chance have negative values in your count files? (not sure how this could happen though)
i didnt change any of the settings. For i DE when i changed turn off outliers to yes the error was solved. but not to other files
Please explain how you preprocessed the data (including code). Did you do any batch correction that changed the raw counts?
after aligning with bowtie i took count table from featurecounts.
The count should not be in negative. The count range from 0 to infinite and not in negative. Please check the input file and remove all negative value into zero.
i checked the whole count files. but can't see any negative values. all the values are 0 and >0.
Thank you all for your kind replies. I found the mistake in my input file. the deseq tool read my gene name in the count table, which in some cases ended in hash 2 as -2. When I gave another feature type in featurecounts the problem was solved.