Question: u133aaofav2 platform gcrma Normalization
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gravatar for samane.khoshbakht
3 months ago by
samane.khoshbakht0 wrote:

hi every body, I am going to use gcrma normalization for a u133aaofav2 platform (Cmap data). but when I use function gcrma(), the following error appear. "Environment u133aaofav2probe was not found in the Bioconductor repository."

I searched the error but I couldnt find any answer for my problem. there is no package for u133aaofav2 probe annotation. I would be greatfull if some one could help me.

annotation gcrma u133aaofav2 • 101 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by samane.khoshbakht0

This has been asked here before. As far as I know Affymetrix has never released the probe information file for this array, and therefore it could not made available at Bioconductor. gcRMA normalization is thus not possible (in principle). See e.g. here: link.

However, it has been suggested by some (reliable) people that the u133aaofav2 array was an early release version of the HT-HG-U133A array. See here. If you are adventurous, you may want to 'convert' (see here) the CEL type from u133aaofav2 to HT-HG-U133A, for which a probe file is available (here).

Lastly, I don't know what you intend to do with these arrays, but please be informed that some (all?) Connectivity Map data is already available at Bioconductor (here). In this context, also this thread may be of relevance.

ADD REPLYlink modified 3 months ago • written 3 months ago by Guido Hooiveld2.5k
Answer: u133aaofav2 platform gcrma Normalization
0
gravatar for samane.khoshbakht
3 months ago by
samane.khoshbakht0 wrote:

Dear Guido Hooiveld, Thank u for complete answer . I will check your suggested links . I found a annotation Excel File in http://girke.bioinformatics.ucr.edu/longevityTools/mydoc/mydoclongevityToolseDRUG_05.html

I will check ConnectivityMap package and I will tell about data. I myself downloaded data from Cmap data link.

ADD COMMENTlink modified 3 months ago • written 3 months ago by samane.khoshbakht0
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