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

[Benilton Carvalho]

Thanks for the heads up, Raffaele.

My suggestion was Javier to try "-a rma" manually, instead of "-a rma- 
sketch" (which appears to be what oneChannelGUI uses - at least that's  
what I saw when skimmed the source ).

cheers,

b

On Nov 12, 2009, at 6:32 AM, rcaloger wrote:

> 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
> tel.   ++39 0116705417
> Lab.   ++39 0116705408
> Fax    ++39 0119038639
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> Info: http://publicationslist.org/raffaele.calogero
>