Hello All,
I have tried ballgown from StringTie on STAR-align->StringTie data results.And with statest I tried get differentially expressed transcripts. But when I take a median between both conditions I see for several transcripts the median is 0 for both condition and still its has p_value less than 0.05 .
And so I classified as DE transcripts. I would like to have Differentially expressed transcripts from the results of StringTie and from the github explannation I have understood Stattest does it . And I wondering how does it works likeDeseq , egeR etc takes fold change into account
. I wonder if you could look and see what the expression values were for that transcript across samples? -->the expression values are also zero across the samples for those transcripts which are identified as Significantly DE ones
That seems very strange that they have entirely zero values but a small p-value. This is just a simple linear model in Stringtie. Can you please post your data/code so I can try to assist?
Jeff
Code is just as it is in GitHub I followed ,
head(pData(bg))
# and then I filtered and annotated the resulted data frame