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

[Dai, Hongying,]

Dr. Carvalho, 

I followed your code and IT WORKS!!! 

Thank you so much! I struggled an entire week trying to get this done. I have tried library(ff) before per Cary Vincent's suggestion. Since I might have other computer issues, library(ff) did not work at the beginning. When I sorted out other computer issues and restarted R, I did not invoke library(ff) as I thought it had been included in library(oligo). 

Again, I really appreciate your help!

Best,

Daisy






-----Original Message-----
From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] 
Sent: Friday, August 12, 2011 1:54 AM
To: Dai, Hongying,
Cc: bioconductor at r-project.org
Subject: Re: [BioC] How to merge to two cel objects imported by oligo package

Hi Daisy,

consider using the following:

library(ff)
library(oligo)
x = read.celfiles(list.celfiles())
exonCore = rma(x, target='core')

This will allow you to read in and preprocess all data at once... It
will be slower, but you will gain from the fact that you're using all
of your samples at once.

About the warning, I need to investigate what is going on. It appears
that you can safely disregard it (but double check the contents of
protocolData(exonCore) ).

b

On 12 August 2011 03:10, Dai, Hongying, <hdai at cmh.edu> wrote:
> 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
>
> Daisy
>
>
>
>
>
>
> -----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)
>
> cheers,
> b
>
> 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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>
>
>
> --
> Successful people ask better questions, and as a result, they get
> better answers. (Tony Robbins)
>



-- 
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)