Question: Deseq2 error,RNA-seq, usegalaxy
0
gravatar for anjuraas
4 months ago by
anjuraas10
anjuraas10 wrote:

hi all 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 DeSeq2

how can i solve this issue? Please help.

rna-seq deseq2 • 239 views
ADD COMMENTlink modified 4 months ago by skjobs012370 • written 4 months ago by anjuraas10

do you by any chance have negative values in your count files? (not sure how this could happen though)

ADD REPLYlink written 4 months ago by lieven.sterck7.3k

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

ADD REPLYlink written 4 months ago by anjuraas10

Please explain how you preprocessed the data (including code). Did you do any batch correction that changed the raw counts?

ADD REPLYlink written 4 months ago by ATpoint32k

after aligning with bowtie i took count table from featurecounts.

ADD REPLYlink written 4 months ago by anjuraas10
0
gravatar for skjobs0123
4 months ago by
skjobs012370
skjobs012370 wrote:

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.

ADD COMMENTlink written 4 months ago by skjobs012370

i checked the whole count files. but can't see any negative values. all the values are 0 and >0.

ADD REPLYlink written 4 months ago by anjuraas10

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.

ADD REPLYlink written 3 months ago by anjuraas10
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