Hello,

I'm working with mouse stem cell and frequently search NCBI GEO datasets for
newly published experiments. Recently I found an experiment on mouse embryonic
stem cell "GSE53275" which is generated on "Affymetrix Mouse Gene 2.1 ST Array
[transcript (gene) version]". I wanted to analyze this dataset but was unable
to normalize the cell files using justRMA() function. Can you please suggest
how to normalize this dataset. Thanks.

You have two choices. You can use either the oligo or xps packages. For oligo, the pipeline is largely similar to the affy package. Assuming you have the celfiles in your working directory, you would do:

library(oligo)

dat <- read.celfiles(list.celfiles())

eset <- rma(dat)

The xps package is an alternative that can do slightly different things than oligo. I am much less familiar, so hopefully Christian Stratowa will be along shortly to show how to use that package. Alternatively, you can search the forum for 'xps AND hugene', or simply look at the vignettes here: http://bioconductor.org/packages/release/bioc/html/xps.html

You could also try the SCAN.UPC package. It should work for this type of array, and you can have it download the files directly from GEO.

Since JIm did mention xps, you can find examples how to use it in directory xps/examples, e.g. script4exon.R.

Best, Christian

Thanks for the reply. It was really helpful. I just have another query. How to do fRMA for "Affymetrix Mouse Gene 2.1 ST Array [transcript (gene) version]"?