Dear list,

 

I am trying to recreate a Figure that I saw in a paper produced with
affycomp.

The Figure is "Figure 5b" where ROC curves show the true/false positives
rate for a set of data summarized with a particular method, using the
LatinSquare experiment of the HGU133A arrays provided by Affymetrix.

 

To summarize my data with GCRMA and then produce the plot, I am running
the following instructions:

 

>library(gcrma);

>

>### then I set the directory where I have the 42 CEL files of the
LatinSquare HGU133A experiment, say "C:/"

>setwd( "C:/")

>

>summarization=justGCRMA();

> write.table(exprs(summarization),file="gcrma.csv", sep = ",",
col.names = NA);

>

>library(affycomp);

>v = read.spikein("gcrma.csv",cdfName="hgu133a");

>g = assessFC2( v , method.name="GCRMA");

>

>affycomp.compfig5b(list(g),method.names=c("GCRMA"));

 

 

Can anyone please tell me if I have skipped a step or if I had done
something wrong ?

Because I simply can't replicate the Figure I want to, and I am just
afraid I might be doing something wrong, or skipping a step.

 

Thank you people.

 

 

Jose Manuel Arteaga

Phd Student in Statistics

University of Essex

UK

 


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