[BioC] different normalized results using oneChannelGUI and oligo packages
Javier Pérez Florido
jpflorido at gmail.com
Tue Nov 10 18:30:17 CET 2009
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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