I want to run Bioconductor packages on mta1.0 affymetrix arrays. I see that there are pd.mta.1.0, mta10stprobeset.db and mta10sttranscriptcluster.db available. There is no workflow for this type of arrays yet availbale. I tried to use affy, and received the message that
The affy package is not designed for this array type. Please use either the oligo or xps package.
Can anyone give me some instructions what should I use, what kinds of files should be present in the current directory? Do I need to upload something from Affymetrix? I do already have mta10 cdf environment.
I built cdf environment for this type of arrays and run the local QC script which requires simpleaffy, affyPLM, affyQCReport, arrayQualityMetrics. It does work fine with mta10cdf environment I provided. It helps me to choose outliers Now I want to run differential expression analysis on the same CEL files of mta1.0 arrays.