[BioC] different normalized results using oneChannelGUI and oligo packages

[Benilton Carvalho]

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 Pérez 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
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
> [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> [5] LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] tools     tcltk     stats     graphics  grDevices utils      
> datasets
> [8] methods   base
>
> other attached packages:
> [1] pd.hugene.1.0.st.v1_3.0.0 oligo_1.10.0
> [3] oligoClasses_1.8.0        oneChannelGUI_1.12.0
> [5] preprocessCore_1.8.0      GOstats_2.12.0
> [7] RSQLite_0.7-3             DBI_0.2-4
> [9] graph_1.24.0              Category_2.12.0
> [11] AnnotationDbi_1.8.0       tkWidgets_1.24.0
> [13] DynDoc_1.24.0             widgetTools_1.24.0
> [15] affylmGUI_1.20.0          affyio_1.14.0
> [17] affy_1.24.0               limma_3.2.1
> [19] Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0 annotate_1.24.0   Biostrings_2.14.0  
> genefilter_1.28.0
> [5] GO.db_2.3.5       GSEABase_1.8.0    IRanges_1.4.0     RBGL_1.20.0
> [9] splines_2.10.0    survival_2.35-7   XML_2.6-0         xtable_1.5-5
>
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