[BioC] options on outputing gene expression based on gene level instead of probe set level for justRMA

[Peter Langfelder]

On Wed, Mar 6, 2013 at 8:48 AM, Jack Luo <jluo.rhelp at gmail.com> wrote:
> Hi,
>
> I am trying to RMA normalize a bunch of cel files and output the gene
> expression matrix to gene level (instead of probe set level), is there any
> option in justRMA that can do this (or any other function that can do
> this?) I searched the options on justRMA, does not seem to have this
> option.

You can output probe-set level data, then use the function
collapseRows in the WGCNA package (CRAN) to summarize probesets for
each gene to a single value.

Best,

Peter