[BioC] Which package for gene expression correlation analysis

[Yuan Hao]

Dear List,

I would like to ask if there is such a bioconductor package available that
can help to achieve the following purpose. Thank you very much in advance!

I got 16 Affy chips corresponding to 4 samples: wild-type treated,
wide-type untreated, knocked-down treated, and knocked-down untreated,
i.e. 4 replicates for each sample.

I want to look at the expression correlations between genes. Say, my gene
of interest is gene X. I would like to find out other genes on the chip
which have the similar expression profiles with gene X across samples. In
other words, if expression levels of gene X increased from wild-type
treated to knocked-out treated, I would like to find all the other genes
have the same trend.

Any comments would be appreciated!

The best,
Yuan