Question: How To Process A .Gpr File Using R And Marray Package Of Bioconductor
0
gravatar for Curious Mind
9 months ago by
Curious Mind0 wrote:

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

ADD COMMENTlink modified 9 months ago by Martin Morgan890 • written 9 months ago by Curious Mind0
0
gravatar for Raygozak
9 months ago by
Raygozak830
State College, PA, Penn State
Raygozak830 wrote:

A simple google search resulted in the following tutorial

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

ADD COMMENTlink written 9 months ago by Raygozak830

Unfortunately it uses limma package and not marray. Thanks

ADD REPLYlink written 9 months ago by Curious Mind0

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.

ADD REPLYlink written 9 months ago by Raygozak830
0
gravatar for Martin Morgan
9 months ago by
Martin Morgan890
Martin Morgan890 wrote:

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)
ADD COMMENTlink written 9 months ago by Martin Morgan890
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