[BioC] affycoretools limma2annaffy output questions

[James W. MacDonald]

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
Hildebrandt Lab
8220D MSRB III
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Ann Arbor MI 48109-0646
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