[BioC] combineAffyBatch problem

[Wolfgang Huber]

Dear Gabor,

you get nonsensical results because you tell justRMA to read two CEL 
files from two different chip types, and to use the CDF annotation of 
yet another third ('virtual') chip type "hgu95a.hgu95av2". You need to 
call these functions with matching sets of probe intensities and CDF; as 
you do in the creation of eset.combcdf1.

  Best wishes
   Wolfgang

> James W. MacDonald <jmacdon at ...> writes:
> 
>> Catherine Dumur wrote:
>>> I understand that every time I run the function, a new .CDF object is 
>>> created and this takes a considerable amount of time. I was wondering if 
>>> we can re-use an existing "newcdf" object when performing new analysis 
>>> where the same two types of arrays are used. In other words, since I am 
>>> always combining the same 2 types Affy chips, the newcdf object should 
>>> be the same. If I use that object from previous sessions, I shouldn't be 
>>> creating a new one every time.
>> You are correct, you _shouldn't_ be creating a new one every time. 
>> Instead, you should save() the newcdf object and load() it back in when 
>> you need it. An example would be:
>>
>> save(newcdf, file="newcdf.Rda")
>> load("newcdf.Rda")
> 
> 
> Dear James & Bioconductor group,
> 
> I'd like to ask a follow-up on the reply you posted here.  You suggested 
> saving and re-loading the new cdfenv environment created by 
> combineAffyBatch, but i can't figure out how to apply the new cdfenv to
> additional AffyBatch objects. In particular, this is wrong:
> 
> -------------------------------------------
> library(affy)
> library(limma)
> library(hgu95acdf) 
> library(hgu95av2cdf)
> library(matchprobes)
> library(hgu95aprobe)
> library(hgu95av2probe)
> 
> targets <- c("GSM44138.CEL", "GSM44275.CEL")
> affyObject1 <- ReadAffy(filenames=targets[1])
> affyObject2 <- ReadAffy(filenames=targets[2])
> 
> res <- combineAffyBatch(list(affyObject1, affyObject2),
> probepkg=c("hgu95aprobe", "hgu95av2probe"), newcdf="hgu95a.hgu95av2")
> 
> hgu95a.hgu95av2 <- res$cdf
> 
> eset.combcdf1 <- rma(res$dat)   ###correct
> eset.combcdf2 <- justRMA(filenames=targets, cdfname="hgu95a.hgu95av2")
> #NOT correct
> -------------------------------------------
> 
> The last line executes without complaint, but the expression values of 
> eset.combcdf2 are completely wrong (i.e. completely uncorrelated with 
> the results of simply doing rma() on the CEL files individually). 
> 
> So my question: why is the last line in the code wrong, and how do i
> correctly reuse the combined cdf environment?
> 
> Thank you!  
> 
> Gabor
> 
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-- 

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber