Question: cufdiff output-cutoff pvalue and parameters for differential expression
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22 months ago by
nishashoolini.phd0 wrote:

dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run cufffidff. in cuffdiff output for studying which genes are differntially expressing what all parameters should be taken care of. i came across one thing from other posts that p value < .05. what other facotrs i should look for before filtering my genes of interest. significant column?? if it says no and p value is less than .05 then can i take that. also how to interpret from promoter diffenrential expn file and tss differential expn file. thanks in advance

significant pvalue cuffdiff • 678 views
ADD COMMENTlink modified 22 months ago by Devon Ryan1.9k • written 22 months ago by nishashoolini.phd0
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22 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Ignore the p-value, you want the q-value instead (this is the p-value adjusted for multiple testing). The "significant" column will then correspond to the q-value. In addition, you may want to filter according to the fold-change (log2(FPKMy/FPKMx)), since values closer to 0 are less likely to be biologically interesting.

Unless you have a burning question, I would suggest only looking at the gene-level differences. All the other stuff is best ignored (both because it's less reliable and also because it's hard to determine what it would biologically mean).

ADD COMMENTlink written 22 months ago by Devon Ryan1.9k
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