[BioC] p values of significant genes in SAM

[Saurin D. Jani]

Hi,

You can P-values and Q-values as below:

sam_p_values <- as.matrix(samoutput at p.value[myDEGenes]);
sam_q_values <- as.matrix(samoutput at q.value[myDEGenes]);

Replace myDEGenes with character set of All Genes and  you can get 
output of all
p-values or q-values of the genes or probeIDs.

Saurin


Quoting Assa Yeroslaviz <frymor at gmail.com>:

> Hi,
>
> i've got a problem extracting the p values of my significance genes.
> I did a sam analysis and want to see the p values of all of the genes and
> only of the sig. genes.
> I did
>
>> samresult at p.value
> to get all my p values.
>
> but I just can't get the command to extract only the p values of my sig.
> genes.
>
> first try was :
>> samresult at mat.sig$p.value
> NULL
>
> second try:
>> samresult at mat.sig[,"p.value"]
> Fehler in "[.data.frame"(samList at mat.sig, , "p.value") :
>        nicht definierte Spalten gewählt
>
> It seems i just can't connect the mat.sig and the p.values columns of my
> data.
>
> I would like to have a table/ matrix with the names of the genes and the
> pvalues of this genes. If it is possible I would also like to have the FDR
> of this list.
>
> I would be very happy to get some help here.
>
> THX
>
>
> Assa
> --
> Assa Yeroslaviz
> Loetzener Str. 15
> 51373 Leverkusen
>
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>
>