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 :
>
>
>
>
>
>
>
>
>
>  ID_REF
>
>  GSM159172
>
>  GSM159173
>
>  GSM159271
>
>  GSM159272
>
>
>
>
>
>  AFFX-BioB-3_at
>
>  88.00277
>
>  76.18801
>
>  74.70855
>
>  78.48763
>
>
>
>
>
>  AFFX-BioB-5_at
>
>  64.32276
>
>  57.14953
>
>  56.92367
>
>  58.82795
>
>
>
>
>
>  AFFX-BioB-M_at
>
>  89.22734
>
>  89.86254
>
>  88.61163
>
>  82.42649
>
>
>
>
>
>  AFFX-BioC-3_at
>
>  298.9344
>
>  246.6433
>
>  303.7554
>
>  248.4071
>
>
>
>
> Thanking you,
> yours faithfully,
> Chittabrata Mal
> JRF, Calcutta university,
> Kolkata, India
>
>        [[alternative HTML version deleted]]
>
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>



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