[BioC] microarray analysis query

[Steve Lianoglou]

Hi,

In general -- it's nearly impossible to try and figure out what
problems you are having because your questions are quite vague. Please
put a more elaborate email together explaining what you are trying to
do.

There are many things involved in "microarray analysis," and saying
that you are having problems with "microarray analysis" without being
more specific leaves us guessing as to what you mean.

It sounds like you would do well to read some of the introductory
texts/vignettes.

The primer "affy" vignette would help:

R> vignette('affy', package='affy')

As too would the limma user guide

R> library(limma)
R> limmaUserGuid()

Please take the time to read those.

Also, read through another example workflow here:
http://www.bioconductor.org/help/workflows/oligo-arrays/

More inline:

On Wed, Apr 13, 2011 at 3:10 AM, Umme Rummana <mbi_umme at yahoo.com> wrote:
> Respected Sir/ Madam,
>  We the students of M.Sc.(BIOINFORMATICS), C.S.J.M. University, Kanpur (U.P),
> INDIA are encountering following problems regarding Microarray analysis while
> using R-Package

Which "R-Package"?

>        1. What are covdesc.txt file?

Where do you see the covdesc.txt file mentioned? (maybe you're trying
to use limma?)

Googling for "covdesc" I see

>        2. How to create & where to save this covdesc.txt file in
> Bioconductor(R-package)?

I still don't know what it is, but you would likely create it with a
"normal" text editor (as in *not* Microsoft Word).

>        3. How to change the cel files into readable format & from where  we can
> download cel files in readable format?

The "affy" primer/vignette talks about loading cel files, as do many others.

You can get cel files from many places, try GEO.

You'd probably prefer the "raw" cel files that you could load into R.
After proper normalization etc. you can them output them in "readable"
format if you want them for something else.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact