On Mon, Mar 31, 2014 at 5:23 PM, BEN HAMDA Cherif
<cherifbenhamda@gmail.com>wrote:

> Hello
>
> I'm starting with R and Bioconductor.
> and usually I analyze .cel files.
> this time I have to do the analysis with gds.soft.gz and serie.matrix
> files.
>

These files contain data as provided by the submitter.  You will need to
read the metadata or, in some cases, write to the submitter to determine
what type of normalization or preprocessing has been done.


> I need advice:
> - Wich  package we use for preprocessing, normalization, filtering and
> analysis this type of files.
>

There is no standard workflow since the information in these files is not
standardized.  However, GEOquery is designed to make getting the data from
GEO into standard bioconductor objects like ExpressionSets.  Once available
in Bioconductor objects, you'll have to define for yourself the best path
forward, but tools like limma are often involved.

Sean



>
> - There is Tutoriel or Workflow ?  which allows me to understand the
> difference between this type of file and to know what are the bioconductor
> packages that I should use.


> Waiting your response, thank you very much
>
> Best
> Cherif
>
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