How To Process A .Gpr File Using R And Marray Package Of Bioconductor

Question

[Curious Mind]

Hi,

This is a bioinformatics question involving R. I am a new bee in R and Bioconductor. I am a new bee in R and Bioconductor. I have a .gpr file from GenePix experiments. I want to load this file using marray package of Bioconductor and extract the foreground and background median values from the Cy5 and Cy3 channels. I was able to load the file. But need help in extracting the above mentioned subset of data.

dat<-read.GenePix(fnames="KLM675590.gpr", path="C:/MyMicroArrays/Data/")

Most of the samples I see on the internet are based upon the swirl dataset, which is loaded when marray package is loaded automatically. I don't see any sample where a .gpr file is processed.

Thanks

Answer 1

[Raygozak]

A simple google search resulted in the following tutorial

http://www.computing.dcu.ie/~asirbu/R.pdf

[Curious Mind]

Unfortunately it uses limma package and not marray. Thanks

[Raygozak]

You can use the str function when in doubt

str(dat)

it will give you the structure of your object and you can get an idea of how you can access the members of the object.

Answer 2

[Martin Morgan]

It's better to ask Bioconductor questions on the Bioconductor mailing list (no subscription required) rather than cross-posting (which is frowned upon!) to StackOverflow and Biostars. From looking at the help page ?read.GenePix and class?marrayRaw I think you can extract, e.g., green background intensities as a plain old matrix and calculate per-sample medians with

apply(maGb(dat), 1, median)