[BioC] RMA, d-chip and Plier for new chip type Human/Mouse/Rat Gene 1.0 ST Array

Fang, Hong* hong.fang at fda.hhs.gov
Fri Feb 22 21:58:10 CET 2008

Dear Sir/Madam:

Thank you very much in advance for your help !

Mr. Robert Gentleman instructed me to contact you (Bioconductor mailing
list)to ask for help regarding Library of new chip types
(Human/Mouse/Rat Gene 1.0 ST Array) in Bioconductor R.

Our ArrayTrack, an FDA microarray software, relay on your Bio-conductor
to convert affy cel file to probe sets file. However, we found that
Human/Mouse/Rat Gene 1.0 ST Array types are not in your R library.


The design of Affymetrix array types Human/Mouse/Rat Gene 1.0 ST Array
is very different from the older ones. One of the key changes is that no
matching MM probes are used for every PM probe. So, the absence of MM
probes has implication for some summarization algorithms and also affect
background subtraction procedures. For example, MAS5 implemented in
Bioconductor are affected by the change. Therefore, MAS 5 algorithms can
not be run on the Exon and Gene arrays. However, RMA, d-chip and plier
should still be OK . We could manually download the corresponding CDF
file from affy's web site and then read the CDF into R, and then run
rma() etc. However, it will not meet customers request to download cdf
file from your library automatically.

We believe you  have been working on it! Nerveless, We would like to
know when Human/Mouse/Rat Gene 1.0 ST Array cdfs files would be
available to the public? Therefore we will anticipate it.

Thank you so much for your rich resources! we all benefit from
Bioconductor R programs!

We are looking forward to your help!!!

Best Regards,


Dr. Hong Fang 
Senior Technical Specialist
Manger, Bioinformatics 
ICF International at NCTR 
National Center for Toxicological Research (NCTR) 
Food and Drug Administration (FDA) 
3900 NCTR Road 
Jefferson, AR 72079 

Tel: 870-543-7538 
Fax: 870-543-7382 
Fax: hong.fang at fda.hhs.gov 

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