Hi,

I want to do a normalization and a differentialy expressed gene list with this study: Series GSE46632

This article tested 3 types off cell line with JIB04 and hybridized the extracted RNA on two microarray. On the GEO there is two WG6 microarray GPL6884 and GPL 3376. On the firts microarray theyve hibridyzed RNAs from HBEC and HCC cell line and on the other microarray they hibridyzed the RNAs from H358 cell line. Do I work with these files together or u cant do that with two diferent array platforms, and I have to do the normalize, lmFit etc separately with the GPL6884 and then with the GPL 3376. Or is the GPL3376 data is the ctrl data like:

 read.ilmn(files='GSE46632_GPL6884_non-normalized.txt', ctrlfiles='GSE46632_GPL13376_non-normalized2.txt', other.columns= 'Detection Pval', sep='\t', probeid= 'ID_REF', expr= 'H')    #???

#In the GPL13376 txt Ive changed the corresponding column names to 'Detection Pval'

So Im confused that there is two txt files and that there is two columns for each sample a Detectopn Pval and a geneexpression raw data.

How do I read it in R? Than do I normalize with normalizeBetweenArrays?

Thanks,

Anna