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

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 > >> 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor