[BioC] Query regarding Bioconductor package

[Sean Davis]

On Sat, Apr 3, 2010 at 1:50 AM, varpal singh <gilvarpal at gmail.com> wrote:
> Respected Mam/Sir,

Hi, Varpal.

> Myself Varpal singh from india, am doing a project on microarray data
> analysis by bioconductor package but am not able to interpretate results. I
> want to analysis Affymetrix data by bioconductor. I got result by running
> the following commands:

What commands?  What is the output of sessionInfo()?  Have you read
the posting guide?  It will help you to get the best answers to your
questions.

> I have a wild and a mutant types each have two replicate i.e Two for wild
> and two for mutant.
>
> I got only 137 genes. after the cut-off 0.001 for p value.

We do not know what would be expected given the biology and we do not
know what analysis was done.  Also, it isn't clear what the p-value
represents.  Is it corrected for multiple tests?

> The result that you can see in the folowing attached excel files, in which
> you can see the fold change value that i dont understand,

File attachments are not included.

> Can we predict up/down regulated genes on the basis of Fold change value ??

A fold change greater than 1 means upregulation and less than 1 means
downregulation.  In log space, this will correspond to >0 and <0
respectively.

> How is it calculate fold change between four CEL files ???

You haven't told us enough information to give you a detailed answer,
but it will be something like the (average of one group)/(average of
the other group).

> Is it use average of wild type replicates and mutant type replicates ??

It sounds like you may need to get some statistics guidance, as
understanding the answers to the questions above are intrinsic to any
microarray analysis.  I would recommend seeking out such a
collaborator, if for no other reason than to learn a bit more about
microarray analysis.

Sean