[BioC] some basic questions

[Sean Davis]

On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest]
<guest at bioconductor.org> wrote:
>
> Hi all..
>
> i have following questions.
>
> 1) How many probesets represent a gene on microarray chip ?
>

That depends on the array platform.  For a given platform, you can use
the annotation packages to answer this question.  To get started, take
a look at:

http://bioconductor.org/help/workflows/annotation-data/

> 2) How do i access raw intesity value of probes (before normalization) ?

This will depend on the array platform and the software package you
are using to do your analysis.  Some specifics are probably needed.
To get started, be sure to take a look at:

http://bioconductor.org/help/workflows/oligo-arrays/

> 3) Do i need to read cdf file to do that ??

Generally not.  Depending on the software package that applies, the
data from the CDF file are usually repackaged for use in bioconductor.
 Again, some specifics of your data and experiment are important.

> 4) After pre-processing the data and normalization, we generally go for significance tests and gene grouping. My question is, if i group the genes before performing  significance test (say now i have 3 groups based on apoptosis,cell cycle, DNA replication) and then perform significance test within each group, will the results be same as that of conventional way ?? Is it a valid method to do so??
>

You might take a look at this question and response on biostar:

http://biostar.stackexchange.com/questions/14796/gene-expression-analysis-microarrays-geneset

Hope that helps.

Sean


> Sorry if my questions are silly.
>
>  -- output of sessionInfo():
>
> --NONE--
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>