Hello, I work on Affymetrix Human Exon 1.0 ST. I trie different methods to analyze this type of microarrays. For the moment, I tried APT and Oligo package: - I did a RMA in APT with this code: apt-probeset-summarize -a rma -p HuEx-1_0-st-v2.r2.pgf -c HuEx-1_0-st-v2.r2.clf -s HuEx-1_0-st-v2.r2.dt1.hg18.core.ps -qc-probesets HuEx-1_0-st-v2.r2.qcc -o OUT_EXON_CORE *.CEL - I did a RMA in Oligo package with this code: library("oligo") library("pd.huex.1.0.st.v2") celFiles <- c("Data GSE24976/GSM613529.CEL", "Data GSE24976/GSM613530.CEL", "Data GSE24976/GSM613531.CEL", "Data GSE24976/GSM613532.CEL", "Data GSE24976/GSM613533.CEL", "Data GSE24976/GSM613534.CEL", "Data GSE24976/GSM613535.CEL", "Data GSE24976/GSM613536.CEL") core_rma = rma(data_base, target = "core") data_base_rma = exprs(core_rma) When I compare the difference of probesets between the normalized file with Oligo package and the normalized file with APT, there is a big difference: - At CORE level: * APT: 287 329 probesets * Oligo package: 22 011 probesets - At FULL level: * APT: 1 384 231 probesets * Oligo package: 266 405 probesets - At EXTENDED level: * APT: 807 038 probesets * Oligo package: 133 672 probesets Why this difference? This difference of probesets between these two methods could be explained by an incomplete information in pd.huex.1.0.st.v2 package? Oligo package is really recommanded to analyse Affymetrix Exon Array? Which package can I use in order to analyze Affymetrix Exon Array at CORE/FULL/EXTENDED level? Thank you for advance for your answer and your help. ------------------------------ My Session Info: R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2 DBI_0.2-5 [4] oligo_1.22.0 oligoClasses_1.20.0 affy_1.36.0 [7] gplots_2.11.0 MASS_7.3-18 KernSmooth_2.23-7 [10] caTools_1.13 bitops_1.0-4.1 gdata_2.12.0 [13] gtools_2.7.0 geneplotter_1.36.0 lattice_0.20-6 [16] annotate_1.36.0 AnnotationDbi_1.20.2 Biobase_2.18.0 [19] BiocGenerics_0.4.0 limma_3.14.1 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 BiocInstaller_1.8.3 [4] Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 [7] ff_2.2-9 foreach_1.4.0 GenomicRanges_1.10.2 [10] IRanges_1.16.3 iterators_1.0.6 parallel_2.15.1 [13] preprocessCore_1.20.0 RColorBrewer_1.0-5 splines_2.15.1 [16] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 [19] xtable_1.7-0 zlibbioc_1.4.0 -- Sophie LAMARRE Statistician - FRANCE [[alternative HTML version deleted]]

I'm not sure how you calculated the number of probesets, but I noticed that you are listing more probesets for "extended" than "full" for APT. You may have gone wrong here somewhere, as there should be more probesets in "full" than in "extended". See here: http://www.affymetrix.com/support/help/exon_glossary/index.affx I.e. "full" includes all the "extended" probesets, but also adds some from computational predictions.... Paul. On Fri, Oct 26, 2012 at 8:39 AM, Sophie Lamarre <sophie.lamarre at="" insa-toulouse.fr=""> wrote: > Hello, > > I work on Affymetrix Human Exon 1.0 ST. > > I trie different methods to analyze this type of microarrays. For the > moment, I tried APT and Oligo package: > - I did a RMA in APT with this code: > apt-probeset-summarize -a rma -p HuEx-1_0-st-v2.r2.pgf -c > HuEx-1_0-st-v2.r2.clf -s HuEx-1_0-st-v2.r2.dt1.hg18.core.ps > -qc-probesets HuEx-1_0-st-v2.r2.qcc -o OUT_EXON_CORE *.CEL > - I did a RMA in Oligo package with this code: > library("oligo") > library("pd.huex.1.0.st.v2") > celFiles <- c("Data GSE24976/GSM613529.CEL", > "Data GSE24976/GSM613530.CEL", > "Data GSE24976/GSM613531.CEL", > "Data GSE24976/GSM613532.CEL", > "Data GSE24976/GSM613533.CEL", > "Data GSE24976/GSM613534.CEL", > "Data GSE24976/GSM613535.CEL", > "Data GSE24976/GSM613536.CEL") > core_rma = rma(data_base, target = "core") > data_base_rma = exprs(core_rma) > > When I compare the difference of probesets between the normalized file > with Oligo package and the normalized file with APT, there is a big > difference: > - At CORE level: > * APT: 287 329 probesets > * Oligo package: 22 011 probesets > - At FULL level: > * APT: 1 384 231 probesets > * Oligo package: 266 405 probesets > - At EXTENDED level: > * APT: 807 038 probesets > * Oligo package: 133 672 probesets > > Why this difference? This difference of probesets between these two > methods could be explained by an incomplete information in > pd.huex.1.0.st.v2 package? > > Oligo package is really recommanded to analyse Affymetrix Exon Array? > Which package can I use in order to analyze Affymetrix Exon Array at > CORE/FULL/EXTENDED level? > > Thank you for advance for your answer and your help. > > > ------------------------------ > > My Session Info: > > R version 2.15.1 (2012-06-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2 DBI_0.2-5 > [4] oligo_1.22.0 oligoClasses_1.20.0 affy_1.36.0 > [7] gplots_2.11.0 MASS_7.3-18 KernSmooth_2.23-7 > [10] caTools_1.13 bitops_1.0-4.1 gdata_2.12.0 > [13] gtools_2.7.0 geneplotter_1.36.0 lattice_0.20-6 > [16] annotate_1.36.0 AnnotationDbi_1.20.2 Biobase_2.18.0 > [19] BiocGenerics_0.4.0 limma_3.14.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affyio_1.26.0 BiocInstaller_1.8.3 > [4] Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8 > [7] ff_2.2-9 foreach_1.4.0 GenomicRanges_1.10.2 > [10] IRanges_1.16.3 iterators_1.0.6 parallel_2.15.1 > [13] preprocessCore_1.20.0 RColorBrewer_1.0-5 splines_2.15.1 > [16] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 > [19] xtable_1.7-0 zlibbioc_1.4.0 > > -- > > Sophie LAMARRE > > Statistician - FRANCE > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com