[BioC] affybatch object too big

James W. MacDonald jmacdon at med.umich.edu
Mon Jun 14 22:49:23 CEST 2010

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.


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:


If you are on Windows or Linux, you could use RMAexpress, which is a 
standalone software to do RMA.




> best regards,
> Noemi
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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