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Old 01-24-2015, 01:26 AM   #1
Junior Member
Location: India

Join Date: Nov 2013
Posts: 2
Default P-Val not significant for diff expressed genes

Dear All,
I have doubt regarding P-Val of diff expressed genes. kindly help
Doubt : I have list of genes which have p-val not significant (>= 0.05) and all the genes are diff expressed (log 2 FC >= 1 or Log2FC <= -1).
Number of the genes is very huge (~3.5k). looking at the Log2 of all these genes, they are diff expressed then why p-val are not significant ? How the p-val been calculated for diff expressed genes? Which factors are taking in the consideration in p-val calculation for diff exp genes?
Here, if i consider p-val (<= 0.05 )for the diff exp genes then probably I miss the many genes which are truly diff expressed.
These results are generated through DESeq.I have also tried cuffdiff for this data and same results i got from there also
FYI : I don't have any technical replicants for this data
Please give your inputs and possible explanation
Ant help would be appreciated
Thank you
chirag.parsania is offline   Reply With Quote
Old 01-24-2015, 08:23 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

This has nothing to do with differential expression, rather it's a failure to understand basic statistics. In short, fold-change isn't an effect size. It has no incorporation of variance, by it's vary nature. However, the reliability of a measurement is dependent on both the fold-change and the variance.
dpryan is offline   Reply With Quote

cuffdiff, deseq, rnaseq

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