How to proccess Microarrays CEL file byR package "oligo" ?

Question

[takoyaki]

Hello, everyone.

I tried micro array analysis by R library "affy", but I got error like this.

eset <- mas5(hoge)

background correction: mas

PM/MM correction : mas

expression values: mas

background correcting...Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered:

Specified environment does not contain HuGene-1_1-st-v1 Library - package hugene11stv1cdf not installed Bioconductor - hugene11stv1cdf not available

So, I decided to use oligo instead of affy. (there was also warning to use oligo or xps)

I just want to normalize by either mas5 or RMA, and then out put normalized CEL file as text file.

Does anyone know how to do above proccess by "oligo" ?

Also, if there is good website about this proccess by oligo, please tell me that URL.

Thank you !

Answer 1

[Kevin Blighe]

It looks like your array is a 'ST' array. These ST arrays do not contain mismatch probes (mostly) and are fundamentally designed differently from other Affymetrix microarrays. You cannot use affy to process these, nor can you use mas5 normalisation.

Using oligo and RMA normalisation is the correct approach.

Just follow the oligo manual and you will be fine: https://www.bioconductor.org/packages/release/bioc/vignettes/oligo/inst/doc/oug.pdf

Once you read in and normalise your data, everything else is mostly the same.

Kevin

[takoyaki]

Thank you so much ! I will read it.