[BioC] different normalized results using oneChannelGUI, and oligo packages

rcaloger raffaele.calogero at gmail.com
Thu Nov 12 09:32:34 CET 2009


Hi,
dear Benilton,
you are right oneChannelGUI uses sketch-quantile. APT-tools are used by oneChannelGUI to calculate intensities.
Actually oneChannelGUI uses a graphical interface to execute 
apt-probeset-summarize -a rma -p PGFFILE.pgf -c CLFFILE.clf  -m  MPSFILE.mps -out rmasketch *.cel
cheers
Raffaele 


>Javier,

>my knowledge on the oneChannelGUI is pretty limited, but it seems to  
>me that it does either rma-sketch or iter-plier.

>oligo will do the "regular" rma, ie. no sketch normalization. Now, if  
>you could download APT and run it yourself (I'm not sure how it is  
>packaged in oneChannel), you could try the following:

>apt-probeset-summarize -a rma -p PGFFILE.pgf -c CLFFILE.clf  -m  
MPSFILE.mps -out rmasketch *.cel

>And you may get more similar results... I'm not saying they'll be  
>identical, but when I implemented this for oligo the mean relative  
>difference between oligo and APT was something like 0.001.

b

On Nov 10, 2009, at 3:30 PM, Javier P?rez Florido wrote:


> > Dear all,
> > I have normalized a GeneChip Human Gene ST 1.0 dataset using oligo
> > package and oneChannelGUI. I've checked that the log2 normalized  
> > values
> > are different (not so different, but different). When applying limma  
> > on
> > them, the statistic values (p-value, M, B and statistic t) are also
> > different.
> >
> > I've read that oneChannelGUI uses APT tools to summarize data and,
> > maybe, that is the point: they produce similar but different  
> > normalized
> > values that have an effect in the final list of differentially  
> > expressed
> > genes.
> >
> > For oligo, I've normalized using rma method and core as a target:
> > OligoEset<-rma(OligoRaw,target="core")
> > For oneChannelGUI, I've used the option "Load gene 1.0 ST arrays from
> > .CEL files."
> >
> > In both cases, the limma parameters are the same.
> > So, I suspect the APT tools used by oneChannelGUI has influence on the
> > data. Is there a way to normalize the raw data in OneChannelGUI to
> > select the subgroup (core) instead of using APT tools? I think this is
> > only available in Exon Arrays.
> >
> > Or may be I am wrong with these conclusions.
> > Any tips?
> > Thanks,
> > Javier
> >
>   
-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
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email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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