Question: Deseq2 error,RNA-seq, usegalaxy
0
gravatar for anjuraas
5 days 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 • 86 views
ADD COMMENTlink modified 2 minutes ago by skjobs012340 • written 5 days 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 5 days ago by lieven.sterck6.4k

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 5 days 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 5 days ago by ATpoint26k

after aligning with bowtie i took count table from featurecounts.

ADD REPLYlink written 5 days ago by anjuraas10
0
gravatar for skjobs0123
2 minutes ago by
skjobs012340
skjobs012340 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 2 minutes ago by skjobs012340
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