HTA 2.0 (Human Transcriptome Array 2.0 - Affymetrix) analysis tools/pipeline?
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8.2 years ago
Rm 8.2k

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

hta 2.0 affymetrix R analysis • 8.3k views
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7.4 years ago

Hi, concerning the oligo package for HTA-2 chip, this tutorial there is a short tutorial has worked perfectely 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!

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

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