[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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