[BioC] Bioconductor Digest, Vol 87, Issue 10

[Richard Pearson]

Hi Avinash

Please read the posting guide and provide a reproducible example and output of sessionInfo().

I'm guessing you don't have replicates of your conditions, and hence the error, but 
difficult to say without knowing exactly what you've done. Showing the output of pData() 
on your ExpressionSet would help confirm this, as in the following example:

library(pumadata)
data(eset_estrogen_rma)
limmaRes <- calculateLimma(eset_estrogen_rma)
pData(eset_estrogen_rma)

              estrogen time.h
low10-1.cel    absent     10
low10-2.cel    absent     10
high10-1.cel  present     10
high10-2.cel  present     10
low48-1.cel    absent     48
low48-2.cel    absent     48
high48-1.cel  present     48
high48-2.cel  present     48

Best wishes

Richard

avinash gupta wrote:
> List,
>        sir , i have create the object by  downloading CEL file through Array
> Express,now I want to do puma clustering method, for this i use "*puma: a
> Bioconductor package for propagating uncertainty in *
> *microarray analysis*" for guideline, in this method i done pumaPCA
> method,but in the second step "Identifying differentially expressed genes"
> show error  in this command
> limmaRes <- calculateLimma(eset_estrogen_rma)
> show error:
> limmaRes <- calculateLimma(eset_rma)
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>   No residual degrees of freedom in linear model fits
> 
> i don't understand it .Plz mail me any help or suggestion about it .
> 
> Regards
> avinash
> 
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-- 
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
University of Oxford                       Tel: +44 (0)1865 617890
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