[BioC] Bioconductor Digest, Vol 87, Issue 10

[Richard Pearson]

Avinash

Please keep replies on list (reply to all).

You've still not given a reproducible example - I don't know what your object eset_rma 
contains. Also, you've not provided the output of sessionInfo(). However, if eset_rma is 
the output of pumaComb, it will contain a single combined expression value for each 
condition, and therefore I would expect calculateLimma to return an error. If you look in 
the puma User Guide, you should see the following two lines:

 > pumaDERes <- pumaDE(eset_estrogen_comb)
 > limmaRes <- calculateLimma(eset_estrogen_rma)

pumaDE is being applied to a combined ExpressionSet (eset_estrogen_comb is the output from 
pumaComb), whereas calculateLimma is being applied to the non-combined ExpressionSet 
(eset_estrogen_rma is NOT the output from pumaComb). In short, don't run calculateLimma on 
the output of pumaComb.

Best wishes

Richard



avinash gupta wrote:
> sir ,
>         in Puma method  for " Identifying differentially expressed (DE) 
> genes with PPLR method"  , i make the object of pumacomb method,and 
> pumaDres method but in the limma Res  i found the errors that show as:
>  > 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
> 
> plz mail me as soon as possible 
> 
> regards
> avinash 

-- 
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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