In your APT calls, you're not using the MPS files. By calling core/full/extended in oligo, you're summarizing to the transcript level, and you should do the same with APT to get comparable results. Best, b Sent from a mobile device. Please apologise for brevity, spelling and punctuation. Sophie Lamarre <sophie.lamarre@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 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]