On Fri, Nov 13, 2009 at 9:29 AM, amit mandal <amit491@gmail.com> wrote:

> hello,
> This mailing list is .for help and queries regarding specific use of
> Bioconductor packages. You should not direct general queries regarding
> microarray analysis here.
>
> All GEO soft files are *chip-level* normalized i.e. the algo./ procedure
> applied while the scanner reads the chip image. One needs to do an *
> additional* level of normalization to take care of array-to-array variation
> and/ or dye-bias (in case of dual-channel data).
>
> Yes, there are a couple of packages in BioC for doing this. e.g *affy* (
> http://bioconductor.org/packages/2.5/bioc/html/affy.html). You may start
> directly from normalization step as the background correction method/
> chip-level normalization has already been applied.
>
> For more info. visit the BioC repository page.
>
>
> cheers..
> amit m
> Graduate student
> Genomics & Molecular Medicine Lab
> IGIB
>
> On Fri, Nov 13, 2009 at 4:16 PM, chittabrata mal <cbmal@rediffmail.com
> >wrote:
>
> > Respected Sir/Madam,
> >
> > I am a jr research fellow of Calcutta University, India working on
> Systems
> > Biology. I have found GEO soft files in the GEO database. I want to know
> > whether the data are already normalized or not. If those are not
> normalized
> > is it possible to normalize those using Bioconductor? I am providing a
> part
> > of one of the soft file to make my problem clear :
>

You can read the description of the GEO datasets in question, but if you
download the GSE record associated with an experiment, these have typically
been normalized.  That is not to say that one can proceed blindly without
looking for biases in the data, but normalized data is the "default"
available from GEO GSE and GDS records.  If you download raw data files
(.CEL, etc), then you can use bioconductor tools, as Amit suggests, to read
in the raw data, do quality control, and normalization.

As a shameless plug, you might want to look at the GEOquery package for
dealing with GEO data; it might make your life a little easier when trying
to pull GEO data into Bioconductor.

Finally, it is probably worth pointing out that a number of software
packages outside of the Bioconductor realm will directly access the GEO
repository and then allow point-and-click analysis for routine tasks.

Sean

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