jane janes wrote:
> 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.)
No further analysis is possible? Why is that?
> I have some perl programming experience and almost no R.
> I Installed all the chicken related packages I found on the
> bioconductor web site (like chickencdf, chickenprobe, ggahomolgy
> 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
> links to the affymetrix probe description webpages.
> I understand that the R packages behind the webbioc interface must
> supplied with the correctly formated microarray data packages to
> 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
> available R modules and packages?
Possible, yes. Easy, no. You will need an annotation package to add
more links to your webpage. To do so you will need the AnnBuilder
package. Unfortunately, AnnBuilder is only directly applicable to
mouse and rat so you will have to extend it to do chicken, which is a
bit of a stretch for someone new to R.
You can more easily use the biomaRt package to annotate your data, but
you won't be able to use webbioc to do so. Instead you will have to do
things directly from within R. You can make HTML tables that are
similar to what you would get with webbioc using biomaRt and the
annotate package. There is a vignette in biomaRt that shows how to do
such a thing.
In addition, there are various functions in affycoretools that will
allow you to either take an MArrayLM object from limma (a bit more
difficult conceptually than multtest, but useful to learn), or simply
take a vector of probeset IDs and a list of statistics and create HTML
tables fairly easily. Again, there is a vignette in affycoretools that
shows how to do this.
> 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.
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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