Hi Roulin,

Please ask the forum and not personally.

As I mentioned there aretwo ways of doing it,

Either by extracting the MM nad PM values for each of the probes from a
probe-set, or by summarizing the intensity values without normalizing it.

As I wanted one value for each gene, I have chosen the second option. For
that you can use the expresso command, were you set bg.correct and
normalize as FALSE. You than need to choose a pm.correct method and the
summarization method you prefer.

This will give you a table of values for each of the genes and arrays you
are using in an affyBatch (input).

Hope this helps
Assa

On Wed, Apr 18, 2012 at 07:19, Ruolin Liu <ruolin@iastate.edu> wrote:

> Hi Assa,
>
> I am facing the same problem you came across before: For each probe, how
> to extract intensity values along with the probe name from CEL file using
> R. I am haunted by it for quite a while. Could you please tell me the way
> in which you settle it down or, if possible, copy and paste your code. I'll
> appreciate your help.
>
> Thanks for your time,
>
> Ruolin Liu
>

	[[alternative HTML version deleted]]

