HTA 2.0 (Human Transcriptome Array 2.0 - Affymetrix) analysis tools/pipeline?

Question

[Rm]

Can any one suggest open analysis tool (R bioconductor if possible) for the above HTA2.0 arrays

"Puma" and "oligo" ? but not clear with the documentation to use

Answer 1

[Iryna Nikolayeva]

Hi, concerning the oligo package for HTA-2 chip, this tutorial there is a short tutorial has worked perfectly for me: http://homer.salk.edu/homer/basicTutorial/affymetrix.html

I have managed to load it, do the RMA normalisation and the plots. But I actually do not manage to use any other normalisation method (I'm specifically interested by quantile normalisation). I've read about libaffy package for quantile normalisation, but I haven't yet tried it. If anyone has any additional info, that would be helpful!

[Rm]

@Iryna Thanks: Better late than never....