[BioC] extracting significant genes using limma

[Naomi Altman]

Since you used "adjust=fdr", the p-value column of the TopTable are 
the "adjusted p-values" after fdr (which I think of as q-values).

You can either pick some q-value you want to use to select the 
significantly differentially expressing genes, or you can pick some 
number of genes, and report the q-value of the least significant of these.

--Naomi

At 10:17 AM 3/13/2006, Assa Yeroslaviz wrote:
>Hi,
>
>I know this theme is an old one, but I look all over the archives and didn't
>find any help regarding this subject.
>Using Affymetrix chips I compared two groups (Control vs compound) with the
>limma procedure.
>I made an affybatch Object using ReadAffy(), normalised the data with the
>RMA algorithm and fitted a linear model with lmFit.
>
> >affy <- ReadAffy(filenames=vec)
> >eset <- rma(affy)
> >design <- cbind(Control=1,AE0627vsCT=c(rep(0,6),rep(1,4)))
>
>my design matrix looks like that (I have 6 control  and 4 treated arrays):
> > design
>       Control AE143vsCT
>  [1,]       1         0
>  [2,]       1         0
>  [3,]       1         0
>  [4,]       1         0
>  [5,]       1         0
>  [6,]       1         0
>  [7,]       1         1
>  [8,]       1         1
>  [9,]       1         1
>[10,]       1         1
>
>so I don't need any contrast matrix.
>The list is 22,810 genes long. But not all of them can be significant. I
>hope!!!
>
>I sorted the genes with:
> >sig_table <- topTable(fit_e, coef=2, number=6000, adjust="fdr", sort.by=
>"P")
>
>I've chosen 6000 as an arbitrary value, but I still don't know how many
>genes are siginificant.
>
>My question(s) is(are):
>
>1. How do I find out how many genes are significantly differentially
>expressed using a define p-value or FDR?
>     Can I use here the decideTests() function although I don't have any
>contrasts?
>
>2. In SAM one can look for the false discovery rates using the different
>delta-values.
>    Is it possible to set a fixed FDR-Value in Limma?
>    Where Do I find the FDR rates of my significant genes?
>
>3. Is there a possibility (like in SAM) to show the results in a graphic (
>scatter plot etc.)?
>
>Every comment and suggestion would be appreciated!
>
>THX
>
>Assa
>
>--
>Assa Yeroslaviz
>Loetzener Str. 15
>51373 Leverkusen
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111