[BioC] How to merge to two cel objects imported by oligo package

Dai, Hongying, hdai at cmh.edu
Fri Aug 12 04:10:27 CEST 2011

Dr. Carvalho, thank you very much! 

I tried to combine CEL files but I don't have enough RAM(2.75GB).  

R> FS3 <- combine(affyExonFS1, affyExonFS2)
Error: cannot allocate vector of size 300.0 Mb

Then I tried to combine RMA processed data instead of combining CEL files.

R> exonCELs<-list.celfiles(full.names = TRUE)
R> affyExonFS1<-read.celfiles(exonCELs[1:6]) #Read 6 CEL files
R> exonCore1 <- rma(affyExonFS1, target = "core")
R> affyExonFS2 <- read.celfiles(exonCELs[7:12]) #Read 6 CEL files
R> exonCore2 <- rma(affyExonFS2, target = "core")

R> exonCore<-combine(exonCore1,exonCore2)
Warning messages:
1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 6 string mismatches
2: data frame column 'exprs' levels not all.equal

My question: 
(A) Is it okay to ignore the warning message and use the combined rma data, exonCore, for further analysis?

(B) Is there any way to improve "exonCore<-combine(exonCore1,exonCore2)" code?

R > dim(exonCore1)
Features  Samples 
   23332        6 
R > dim(exonCore2)
Features  Samples 
   23332        6


-----Original Message-----
From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] 
Sent: Thursday, August 11, 2011 6:57 PM
To: Dai, Hongying,
Cc: bioconductor at r-project.org
Subject: Re: [BioC] How to merge to two cel objects imported by oligo package

FS3 <- combine(affyExonFS1, affyExonFS2)


On 11 August 2011 18:36, Dai, Hongying, <hdai at cmh.edu> wrote:
> Hi,
> Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now.
> Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works.
> R>biocLite("pd.moex.1.0.st.v1")
> R>biocLite("olig")
> R>exonCELs <- list.celfiles(full.names = TRUE)
> R>affyExonFS1 <- read.celfiles(exonCELs[1:6])  #First read 6 CEL files, then save the results and clear the memory
> R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files
> Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work
> R>library(affy)
> R> merge.AffyBatch(affyExonFS1,affyExonFS2)
> Error in function (classes, fdef, mtable)  :
> unable to find an inherited method for function "intensity", for signature "ExonFeatureSet"
> Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package.
> Thanks!
> Daisy
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