Question: HT_HG-U133A_EA probe tab annotation file
0
gravatar for rv
2.1 years ago by
rv20
rv20 wrote:

Hello everyone, I am searching for the probe tab annotation file for the Affymetrix platform:

ht_hg-u133a_ea

wich is used for some drug assays at Connectivity Map database.

For the hg-u133a and the ht_hg-u133a platforms, which are also used for the assays, I can find the corresponding probe tab file at:

http://www.affymetrix.com/analysis/downloads/data/HG-U133A.probe_tab.zip

http://www.affymetrix.com/analysis/downloads/data/HT_HG-U133A.probe_tab.zip

but I am non able to find such an annotation file for the ht_hg-u133a_ea platform.

Could anyone, please, suggest me a link?

Thanks

microarray connectivity map • 1.1k views
ADD COMMENTlink modified 7 months ago by colinwxl0 • written 2.1 years ago by rv20

In NCBI GEO database, the GPL id is GPL4685. However, I'm not sure whether its probes id in right format. And I don't how to covert it into XXX.db which can be used in R. Can you share with us your final solutions? Please.

ADD REPLYlink written 7 months ago by colinwxl0
1
gravatar for eldronzhou
2.1 years ago by
eldronzhou350
eldronzhou350 wrote:

This link suggests that ht_hg-u133a_ea is referred to as U133AAofAv2. Therefore, you can access the platform with Bioconductor:

source("http://www.bioconductor.org/biocLite.R")
biocLite("u133aaofav2cdf")
ADD COMMENTlink written 2.1 years ago by eldronzhou350

Thank you @eldronzhou for your answer, I was really searching for a textual, tab delimited, file but, yes, I could access the annotation by R. (I could even serialize the R DataFrame into a tab delimited textual file). Yes, thank you, I didn't consider this option.

ADD REPLYlink written 2.1 years ago by rv20

Unfortunately, it seems that the "u133aaofav2cdf" package doesn't contain probe information.

I would be interested in doing, with the "u133aaofav2" platform exactly what is done with the "rae230a" platform in this tutorial:

https://www.bioconductor.org/packages/3.3/bioc/vignettes/annotate/inst/doc/useProbeInfo.pdf

but I cannot find the libraries:

"u133aaofav2.db"

"u133aaofav2probe"

I am specifically interested in the mapping:

array x, y coordinates <-> Probe Interrogation Position

Where could I find such a map for the "u133aaofav2" chip?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by rv20

Well, it seems that the probe file of u133aaofav2cdf is unfortunately not available on the Affymetrix website. And as its name suggests, this particular array is an early access and may be deprecated later on. Maybe you can try to contact the technical support of Affymetrix for probe information.

ADD REPLYlink written 2.1 years ago by eldronzhou350

Ok, thank you very much.

ADD REPLYlink written 2.1 years ago by rv20

Dear rv, did you eventually find the probe file for u133aaofav2cdf?

ADD REPLYlink written 12 months ago by k.k.m.koudijs0
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