[BioC] Variability Plot For Toray Microarray Data

[Steve Lianoglou]

Hello Peverall, Gundalla, and Edward,

Out of curiosity: are you all the same person?

On Wed, Jan 30, 2013 at 8:54 AM, Gundala Viswanath <gundalav at gmail.com> wrote:
>
> Dear Steve,
>
> Thanks for your reply.
>
>
>> The two values that are averaged and "log-fold-changed" in an MA plot
>> for affy arrays array always from datasets that have 2+ arrays. These
>> statistics are either generated across replicates (so 1 array vs
>> another), or sometimes 1 array vs a pseudo-array, which might be the
>> mean expression of the probes across your samples.
>>
>
> Let say I have 4 vectors.
>
> v1.norm
> v2.norm
>
> v1.raw
> v2.raw
>
> Later I want to compare the differential expression between v1 and v2.
> So I want to know whether the normalization I did is acceptable, using MA
> plot.
>
> Does MA plot for (v1.norm and v2.norm) still valid?

If you're still stuck with no replicates between conditions, I'm not
sure how to assess whether one normalization technique is better than
the other.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact