[BioC] vsn on vsn

[Sean Davis]

On Fri, Sep 16, 2011 at 8:07 AM, Dr Balazs Gyorffy <zsalab2 at yahoo.com> wrote:
> The problem is that one of them is Illumina and the other one is Agilent, so
> merging them at the raw data stage is very "hard".

You should probably look at using a meta-analysis method rather than
trying to merge "the numbers".  This type of cross-dataset analysis
can be quite challenging and depends on the details of the two
datasets and the questions one is trying to answer.  Defining how to
do such an analysis in email without a lot more detail is not really
possible.

Sean


> Best:
> Balazs
>
> -------------------------
> Balázs GYÖRFFY MD, PhD
> Research Laboratory for Pediatrics and Nephrology, Hungarian Academy of
> Sciences - Semmelweis University 1st Dept. of Pediatrics
> Bokay u. 53-54., Budapest H-1083
> Office: +36 1 459 1500 /52772
> Fax: +36 1 3036 077
> Email: zsalab2 at yahoo.com
> ________________________________
> Von: Sean Davis <sdavis2 at mail.nih.gov>
> An: Dr Balazs Gyorffy <zsalab2 at yahoo.com>
> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Gesendet: 13:39 Freitag, 16.September 2011
> Betreff: Re: [BioC] vsn on vsn
>
> Hi, Balazs.
>
> You should probably merge at the "raw data" stage and then normalize
> the data together as one batch.
>
> Sean
>
> On Fri, Sep 16, 2011 at 7:29 AM, Dr Balazs Gyorffy <zsalab2 at yahoo.com>
> wrote:
>> Hi All!
>>
>>
>> I  want to merge the two different microarray datasets, one was VSN
>> normalized and the other one quantile-normalized. Can I use a second VSN
>> normalization? Any other normalization / related literature?
>>
>>
>> Thanks:
>>
>> Balazs
>>
>>
>> -------------------------
>> Balázs GYÖRFFY MD, PhD
>> Research Laboratory for Pediatrics and Nephrology, Hungarian Academy of
>> Sciences - Semmelweis University 1st Dept. of Pediatrics
>> Bokay u. 53-54., Budapest H-1083
>> Office: +36 1 459 1500 /52772
>> Fax: +36 1 3036 077
>> Email: zsalab2 at yahoo.com
>>
>>        [[alternative HTML version deleted]]
>>
>>
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