[BioC] affycoretools limma2annaffy output questions
James W. MacDonald
jmacdon at med.umich.edu
Fri Sep 26 14:32:22 CEST 2008
Hi Hui-Yi,
Hui-Yi Chu wrote:
> Hi everyone,
>
> Apologize first for probably simple question below.
> Thanks for Jim's help, I've got some html files from limma2annaffy function,
> however, I am not pretty sure how to interpret the result of "fold change".
> Please correct me if I am wrong. Based on my knowledge, after limma, for
> example in coef=1, the fold change represents the contrast of the expression
> value means from two groups. But the html result made me confused:
>
> The header of html is like this:
> probes Description Pubmed Gene Ontology Pathway t-statistic
> P-value Fold-change array1 array1 array2 array2
>
>
> The question is why the fold change is not really the value that (mean of
> group1)- (mean of group2) ?? If it is because of permutation??
The fold change *is* mean(goup1) - mean(group2). If you show us your
code and a snippet of the output we might be able to help (please see
the posting guide).
> I've read limma user guide and ?limma2annaffycore, so I believe the value of
> array 1 and 2 are expression value.
> By the way, the function of pflt filter genes by p value, but if I want to
> filter gene by adj.p.val??
I don't know of any function pflt. However, if you mean the argument
pfilt, then it *does* filter by adjusted p-value if in fact you are
adjusting the p-value to begin with.
Best,
Jim
>
>
> Thank you very much!!
> Hui-Yi
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
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