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

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

r bioconductor
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updated by Martin Morgan Martin Morgan • written by Curious Mind • Curious Mind

2 answers

A simple google search resulted in the following tutorial

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

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written by Raygozak Raygozak

Unfortunately it uses limma package and not marray. Thanks

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written by Curious Mind • Curious Mind

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.

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written by Raygozak Raygozak

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)
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written by Martin Morgan Martin Morgan

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