R/Bioconductor And .Chp Files

Question

[Lídia]

Hi all I want to extract the level of expression of two genes from the microarray data deposited here. The available files are the following:

Investigation description E-MEXP-1594.idf.txt

Sample and data relationship E-MEXP-1594.sdrf.txt

Raw data (2) E-MEXP-1594.raw.1.zip, E-MEXP-1594.raw.2.zip

Processed data (1) E-MEXP-1594.processed.1.zip

Array design A-AFFY-35.adf.txt

R ExpressionSet E-MEXP-1594.eSet.r

I am completely new to microarray data analysis so I thought that the porcessed data would be the easiest thing to interpret. I downloaded the corresponding folder and it contains many .CHP binary files but I cannot open them. I have read in many forums that R/bioconductor is a suitable software for microarray data analysis so I installed R and bioconductor and the affy package but I still don't know if I can open .CHP files with bioconductor since the reference manual of the affy package doesn't say anything about this files... Is this the easiest way to get the expression of the two genes I am interested in??

I would really appreciate your help!

Answer 1

[AndreiR]

Hi,

Regarding chp format, may you consult these site http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html

About analysing microarray, here you find very good info Analysing microarray data in BioConductor

And more info about the process here http://www.mathworks.com/products/demos/bioinfo/affydemo/affydemo.html

If you want to start from raw files, use archives E-MEXP-1594.raw* where .CEL files are.

Hope it helps

[Lídia]

Thank you! These links were very helpful. Specially the second and third one. At the end I started from the raw files and I could check what I was looking for :D

Answer 2

[Martin Morgan]

I believe that you can install the ArrayExpress package

source("http://bioconductor.org/biocLite.R")
biocLite("ArrayExpress")

do this once. Then in an R session

library("ArrayExpress")
xx = ArrayExpress("E-MEXP")

to download the data and return an ExpressionSet for use in down-stream analysis, e.g., using the package "limma" for differential expression. After loading the ArrayExpress package, see the help page of the ArrayExpress function

?ArrayExpress

and the package vignette

vignette("ArrayExpress")

Consider posting follow-up questions to the Bioconductor mailing list.

[Lídia]

Thank you very much! It was very easy to import the data from ArrayExpress and I could do some basic manipulations following the vignette and the reference manual instructions so at the end I could extract the information I needed.