edgeR: Common dispersion and pseudocounts

flobpf · 07-05-2013, 09:46 PM

Common dispersion will tell me how much variability I should expect, on an average, in a given gene's mean expression value. Is that the variability due to technical effects or biological effects?

Secondly, how does edgeR go from the common dispersion estimate to getting pseudocounts? For example, if the CD is 0.005 and the readcounts of a gene across 2 replicates and 2 treatments are (r1=100,r2=120,x1=500,x2=200), how does edgeR know whether to increase x2 or decrease x1 and to what extent?

Also, at what step are the normFactors used? Are they used in making pseudocounts?

Thanks

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[EdgeR] exactTest dispersion="common"	syintel87	Bioinformatics	0	05-23-2013 07:12 PM
EdgeR condition-specific dispersion	tfwillems	RNA Sequencing	1	10-05-2012 07:21 AM
with or w/o pseudocounts in DESeq?	ekimmike	Bioinformatics	3	10-04-2012 02:19 PM
DESeq Estimate Dispersion	mattia	Bioinformatics	1	02-09-2012 02:42 AM
edgeR with no replication (Common disp or poisson)	sergio	Bioinformatics	3	05-24-2010 09:53 PM

07-05-2013, 09:46 PM	#1
flobpf Member Location: USA Join Date: Apr 2010 Posts: 76	edgeR: Common dispersion and pseudocounts Common dispersion will tell me how much variability I should expect, on an average, in a given gene's mean expression value. Is that the variability due to technical effects or biological effects? Secondly, how does edgeR go from the common dispersion estimate to getting pseudocounts? For example, if the CD is 0.005 and the readcounts of a gene across 2 replicates and 2 treatments are (r1=100,r2=120,x1=500,x2=200), how does edgeR know whether to increase x2 or decrease x1 and to what extent? Also, at what step are the normFactors used? Are they used in making pseudocounts? Thanks Last edited by flobpf; 07-05-2013 at 09:47 PM. Reason: added one more question