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??
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??


Thank you very much!!
Hui-Yi

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