The only package for the HTA2.0 platform is pd.hta.2.0, and it provides only the sequence information for the probes (PM). Manual says it should be used in conjunction with the package 'oligo'.

Does Affy provide annotation? You could use merge on the output of limma with Affy provided annotation.

There should be an annotation file from the HTA website, I cannot obtain the csv file because it requires a login

http://www.affymetrix.com/support/technical/byproduct.affx?product=human_transcriptome

HTA-2_0 Probeset Annotations, CSV Format, Release 34 (48 MB, 1/23/14)

Once you download the file, you can just use the "match" function in R to match them. Or merge like Gerald suggest should be fine

Hi Alejandro,

I am curious to know how did you tackled this issue at the end?

I have the same issue. and tried to follow Gen Lin solution but couldn't figure out how to do it optimally, without opening Affymetrix huge annotation excel sheet.

Thanks in advance.

Hi Hossein, I worked on this a while ago, so I don't remember from the top of my head what I did at the end. However, more recently I've been working with other Affymetrix data and I used their software for the normalisation and to determine which genes are expressed and which are not.

Their software is easy to use and can be downloaded from their website.

Please let me know any questions you may have.

Best wishes