[BioC] How to merge to two cel objects imported by oligo package
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")
1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 6 string mismatches
2: data frame column 'exprs' levels not all.equal
(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)
R > dim(exonCore2)
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:
> 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>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> 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.
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