[BioC] affybatch object too big

[Benilton Carvalho]

and oligo may be of interest too (if the annotation package isn't
online, you'll need to build your own via pdInfoBuilder)...


library(oligo)
library(ff)
cels = list.celfiles()
rawData = read.celfiles(cels)
rmaData = rma(rawData)

## resFF is a ff object
resFF = exprs(rmaData)
resFF[1:10, 1:4]

## if you have RAM to store the exprs matrix
resMatrix = resFF[]

## save in a tab-file
tmp = as.ffdf(resFF)
write.table(tmp, file="results.csv", quote=FALSE, sep="\t")


same applies for Exon and Gene ST arrays.

b

On 14 June 2010 21:49, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Noemi,
>
> Noemi Andor wrote:
>>
>> Hi,
>>
>> I have a problem with the loading of an affybatch object from cel-files. I
>> have multiple cel files and want to analyze them all together, yet the
>> amount of data is to big to be loaded. I am interested only in a subset of
>> genes within those cel-files. So I could load the cel-files into 3 or 4 affy
>> objects, then read the expression values of the genes of interest and merge
>> them again. But if I read them separatly, the background correction wil not
>> be global, and I do not know how to read them without background correction:
>>
>> pd=read.AnnotatedDataFrame("BI_samples_1.txt", header=TRUE, row.names=1)
>> a= ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose =
>> TRUE)
>> eset<-rma(a)
>> e206123_at<-exprs(eset["206123_at"])
>> ...
>> e210684_s_at<-exprs(eset["210684_s_at"])
>> e1<-rbind(e206123_at,..., e210684_s_at)
>>
>> If I do the same for BI_samples_2.txt the corresponding e2 will not be
>> comparable to e1, am I right?
>>
>> Would be very greatfull for a good solution to my problem?
>
> You don't mention your OS, so it is more difficult to suggest. Assuming you
> don't have access to a computer with more memory, the memory-bounded
> solutions are as follows.
>
> The xps package of Bioconductor. Requires installation of ROOT, but the
> maintainer Christian Stratowa is very active and helpful on this list.
>
> You will need to go here first to get ROOT.
>
> http://root.cern.ch/drupal/
>
> then a simple biocLite("xps") should get you started.
>
> A non-BioC but still R based choice is aroma.affymetrix. More info can be
> found here:
>
> http://www.aroma-project.org/
>
>
> If you are on Windows or Linux, you could use RMAexpress, which is a
> standalone software to do RMA.
>
> http://rmaexpress.bmbolstad.com/
>
>
> Best,
>
> Jim
>
>
>
>>
>> best regards,
>>
>> Noemi
>>
>> _______________________________________________
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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