[BioC] webbioc chicken

[James W. MacDonald]

Hi Jane,

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. 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?

No.

> If they do not exist is it possible to be created by using the already
> available R modules and packages?

Possible, yes. Easy, no. You will need an annotation package to add any 
more links to your webpage. To do so you will need the AnnBuilder 
package. Unfortunately, AnnBuilder is only directly applicable to human, 
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 fairly 
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.

Best,

Jim


> 
> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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