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!