[BioC] normalized probes

[James W. MacDonald]

Hi Lana,

 > library(affy)
 > data(affybatch.example)
 > tmp <- normalize(affybatch.example)
 > all.equal(exprs(affybatch.example), exprs(tmp))
[1] "Mean relative  difference: 0.1390075"

 > cbind(pm(affybatch.example, "A28102_at")[,1], pm(tmp, "A28102_at")[,1])
              [,1]     [,2]
A28102_at1  149.0 132.0667
A28102_at2  143.5 127.3167
A28102_at3  132.0 115.8333
A28102_at4  130.0 113.7167
A28102_at5  115.8 100.3667
A28102_at6  131.0 114.4333
A28102_at7  131.8 115.4000
A28102_at8  140.0 123.6667
A28102_at9  122.0 106.3333
A28102_at10 133.3 117.2000
A28102_at11 136.0 120.1000
A28102_at12 123.0 107.3333
A28102_at13 132.5 116.5000
A28102_at14 130.0 113.7167
A28102_at15 125.0 109.0333
A28102_at16 133.5 117.3333

Best,

Jim




Lana Schaffer wrote:
> Hi,
> I am wondering if it is possible to obtain the 
> normalized probe values after quantile normalization.
> I have tried the option of using the destructive=F
> and then looked at the intensity matrix and found the
> values to be unchanged.  
> I would like to know the different between the probe
> matrix and the intensity matrix.  The index/order
> has been changed in the probe matrix from the intensity
> matrix and for my case the number of rows is reduced
> for the probe matrix.
> I will probably need to do the quantile normalization
> separate from RMA to get the probe intensity values?
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623