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?

Sincerely,
Edward



>
> -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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

