[BioC] EdgeR: Using estimateCommondisp for housekeeping genes

Tonya Mariko Brunetti brunettt at unm.edu
Sat Nov 12 23:12:06 CET 2011


My name is Tonya and I am very new to both R and edgeR so 
sorry if this seems silly.  I have recently gotten back 
results of two samples from a 454 and do not have 
replicates of either.  I was reading the edgeR manual 
section about what to do about calculating common 
dispersion factors if no replicates are available.

One of the options was to use genes that are not suppose 
to be differentially expressed (ie housekeeping genes) to 
determine the common dispersion.  In the manaul they show 
an example do<-estimateCommonDisp(d[housekeeping,]).

Would anyone please explain to me how I can use the 
housekeeping genes in the data I have collected to 
estimate this value.  I have tried numerous things for 
input into the function estimateCommonDisp (see below some 
of what I have tried) but I guess I don't know how to 
specify just the housekeeping genes??  Or if anyone has a 
method for common dispersion in edgeR that will work for 
no replicates that would be appreciated as well!

estimateCommonDisp(d['RpS2','RpS28b]) (where the stuff in 
brackets are my housekeeping genes and d is my normalized 

Thank you so much!


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