EBMultiTest -PPDE values for each comparison

bioinfo C

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Apr 14, 2016, 9:19:42 AM4/14/16

to EBSeq users

Hi Everyone,

I am recently trying EBSeq for both multiple comparison and pairwise comparison. I have 5 isolate and I did multiple comparison with EBMultiTest across all the 5 isolates and then did pairwise comparison with EBTest. I got PPDE values for each pairwise comparison but I am not able to get the PPDE value for each comparison in multiple comparison.

Is there a way I can get those values as I want to compare the multiple comparison with pairwise.

And, if anyone can let me know how PPDE is calculated.

Thanks for help!

Ning Leng

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Apr 14, 2016, 11:16:53 AM4/14/16

to bioinfo C, EBSeq users

Hi,
Details of the multiple condition test implementation can be found at
EBseq vignette:
http://bioconductor.org/packages/release/bioc/vignettes/EBSeq/inst/doc/EBSeq_Vignette.pdf
section 5.3 (page 24)
Details of the multiple condition model can be found at supplement of
EBSeq manuscript
http://bioinformatics.oxfordjournals.org/content/suppl/2013/02/21/btt087.DC1/lengetal_supplement_submit.pdf
section 6.2
Hope this is helpful
Best,
Ning

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Ning Leng, Ph.D
Computational Biologist / Biostatistician
Regenerative Biology Laboratory
Morgridge Institute for Research

bioinfo C

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Apr 14, 2016, 11:27:09 AM4/14/16

to EBSeq users, sul...@purdue.edu

Hi Dr. Leng,

Thank you for the reply.

I was able to run the EBMultiTest for multiple comparison using following command:

MultiOut=EBMultiTest(countData1,NgVector=NULL,Conditions=Conditions, sizeFactors=MultiSize,maxround=5)

I got FC values for 10 comparison in FCMat:

FCAvsB FCAvsC FCAvsD FCAvsE FCBvsC FCBvsD FCBvsE FCCvsD FCCvsE FCDvsE

I was wondering can we get the PPDE values for these comparisons when I run EBMultiTest. Because the output of the EBMultiTest has no such output which says PPDE.