[BioC] webbioc chicken

jane janes reymonnn at gmail.com
Mon Feb 19 09:07:54 CET 2007


Dear List,

Recently I installed webbioc on my laptop. It works perfect but our
lab is interested mainly in chicken affymetrix
microarray analysis. (I can use affy and multtest with our chicken
affy CEL files but no further analysis is possible.)
I have some perl programming experience and almost no R. Nevertheless
I Installed all the chicken related packages I found on the
bioconductor web site (like chickencdf, chickenprobe, ggahomolgy etc)
and I tried to make webbioc (annaffy) to work with them by modifying
the cgi scripts.
The only output I have been able to acquire was HTML table containing
links to the affymetrix probe description webpages.
I understand that the R packages behind the webbioc interface must be
supplied with the correctly formated microarray data packages to work
properly but
most probably I have been unable to identify the right files in the
bioconductor repository.
Here are and my questions:
Do such affy chicken files (correctly formatted for webbioc) exist?
If they do not exist is it possible to be created by using the already
available R modules and packages?

Please excuse me if my question is not very well structured but I am
relatively new recruit
in the world of R and bioinformatics.
Thank you very much in advance for your answers.

Vassil



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