[BioC] Annotate Package: How do I get the gene names and how do I write my matrix

[Adaikalavan Ramasamy]

See comments below.

On Wed, 2004-08-18 at 18:54, S Peri wrote:
> Dear group, 
> 
> I did SAM, T-test analyses and obtained p-values. Now,
> these files look like these:
> 
> T-test Values:
> 
> > Gli_X0_X1_pvals[1:5]
>   100_g_at    1000_at    1001_at  1002_f_at  1003_s_at
> 
> 0.80033009 0.31943016 0.33078591 0.05216239 0.08957325
> 
> 
> 
> Fold change(Avg. Diff):
> > MyBrain_X0_X1_Exp_FCs[1:5]
>  100_g_at   1000_at   1001_at 1002_f_at 1003_s_at 
> 1.0176023 0.9274588 0.8752550 1.1056984 1.1096023 
> 
> 
> My question: 
> 
> Using annotation package how can I convert the probe
> ID's to Gene names. how do i incorporate gene name in
> place of 100_g_at?
> 

There are annotation packages in BioConductor. But if you want a
quick and dirty solution, get the CDF file from affymetrix and
merge it in excel. These will have all the information you need
but may be slightly outdated.

Can anyone on the list comment the merits of doing this 
versus using the BioConductor annotation package ?

> 2.  How can I choose/filter P-values from T-test that
> are less than 0.01 to 0 ?

You can write this yourself with a few ifelse(), which(), subset()
commands.

> 3. How can write the values into a table with 3
> colnames:
> Gene, P-value, Fold change

mat <- cbind( genename, pvalue, foldchange )
write.table(mat, file="aaa.txt", sep="\t", quote=FALSE)

> I am doing this for first time. Please help me. 
> 
> Thank you.
> 
> Regards, 
> PS
> 
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