Hello, I have a question regarding XPS and APT when computing DABG option. Here's my XPS command: #begin XPS code dabg.call(root.data, filedir = root.path, filename = paste("tmpdt", "RMA", root.filename, sep="_"), option = "probeset", exonlevel = "all", verbose = TRUE) #end Here's my APT command line: #begin apt-probeset-summarize -a dabg -feat-details -b /Data/affx.tech.files /HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.antigenomic.bgp -p /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf -c /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx- 1_0-st-v2.r2.crosshyb_1.na24.clf -s /Data/affx.tech.files/HuEx- 1_0-st-v2.r2/HuEx-1_0-st-v2.r2.dt1.hg18.full.mps --qc-probesets /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.qcc -o dabg/ --subsample-report --cel-files cel_list.txt #end I get different p-values and different Percent Present calls. (Highly correlated though). #R code cor(apt.detcal$all_probeset_percent_called,xps.detcal$PercentPresent) #[1] 0.9978199 #difference in PSRs between XPS and APT dabg output length(setdiff(xps.dabg[,2], rownames(apt.dabg))) #[1] 15332 #difference in PSRs between APT and XPS dabg output length(setdiff( rownames(apt.dabg), xps.dabg[,2])) #[1] 2904 #Total # of PSRs that differ 2904+15332 #[1] 18236 #PSRs in common length(intersect(xps.dabg[,2], rownames(apt.dabg))) #[1] 1381327 The APT output is always lower in the PercentPresent. Thanks in Advance -- output of sessionInfo(): R version 2.13.1 (2011-07-08) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] xps_1.12.1 abind_1.4-0 survival_2.36-14 [4] affxparser_1.24.0 fastmatch_1.0-4 glmnet_1.7.1 [7] Matrix_0.999375-50 earth_3.2-3 plotrix_3.4-3 [10] plotmo_1.3-2 leaps_2.9 rpart_3.1-50 [13] HDclassif_1.2.1 MASS_7.3-13 randomForest_4.6-6 [16] e1071_1.6 class_7.3-3 oligo_1.14.0 [19] oligoClasses_1.14.0 frma_1.3.10 Biobase_2.12.2 [22] caret_5.15-023 cluster_1.14.0 reshape_0.8.4 [25] plyr_1.7.1 lattice_0.19-30 matrixStats_0.4.3 [28] R.methodsS3_1.4.2 abind_1.4-0 foreach_1.4.0 [31] itertools_0.1-1 iterators_1.0.5 loaded via a namespace (and not attached): [1] affy_1.30.0 affyio_1.20.0 Biostrings_2.20.4 [4] codetools_0.2-8 DBI_0.2-5 grid_2.13.1 [7] IRanges_1.10.6 preprocessCore_1.14.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Zaid, The differences may be caused as follows: - Although you did not mention how you have created the root scheme file I assume that you use the newest Affymetrix annotation files version na32. Please note that these annotation files use human genome build hg19, whereas the file HuEx-1_0-st-v2.r2.dt1.hg18.full.mps uses hg18. - The metaprobeset file HuEx-1_0-st-v2.r2.dt1.hg18.full.mps that you are using is not only based on hg18, but was created on Oct 2006, and is thus completely outdated. To be able to compare APT with XPS you need to create a new metaprobeset file, e.g. using xps function metaProbesets(). - The clf-file you are using, i.e. HuEx- 1_0-st-v2.r2.crosshyb_1.na24.clf is not the official Affymetrix clf-file, which is called HuEx-1_0-st-v2.r2.clf - If you want to lower the number of PercentPresent you can adjust alpha1 and alpha2 to get usable P/M/A calls for transcripts. Please have a look at vignette APTvsXPS.pdf, especially chapter 4.3 where I have compared DABG calls from APT vs XPS. Furthermore, please look at the corresponding script xps/examples/script4xps2apt.R which contains the complete source code used in vignette APTvsXPS. Best regards, Christian On 8/31/12 7:06 PM, zaid haddad [guest] wrote: > Hello, > > I have a question regarding XPS and APT when computing DABG option. > > Here's my XPS command: > > #begin XPS code > dabg.call(root.data, filedir = root.path, filename = paste("tmpdt", "RMA", root.filename, sep="_"), option = "probeset", exonlevel = "all", verbose = TRUE) > > #end > > Here's my APT command line: > > #begin > apt-probeset-summarize -a dabg -feat-details -b /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx- 1_0-st-v2.r2.antigenomic.bgp -p /Data/affx.tech.files/HuEx- 1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf -c /Data/affx.tech.files/HuEx- 1_0-st-v2.r2/HuEx-1_0-st-v2.r2.crosshyb_1.na24.clf -s /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx- 1_0-st-v2.r2.dt1.hg18.full.mps --qc-probesets /Data/affx.tech.files /HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.qcc -o dabg/ --subsample-report --cel-files cel_list.txt > > #end > > I get different p-values and different Percent Present calls. (Highly correlated though). > > #R code > cor(apt.detcal$all_probeset_percent_called,xps.detcal$PercentPresent) > #[1] 0.9978199 > > #difference in PSRs between XPS and APT dabg output > length(setdiff(xps.dabg[,2], rownames(apt.dabg))) > #[1] 15332 > #difference in PSRs between APT and XPS dabg output > length(setdiff( rownames(apt.dabg), xps.dabg[,2])) > #[1] 2904 > #Total # of PSRs that differ > 2904+15332 > #[1] 18236 > #PSRs in common > length(intersect(xps.dabg[,2], rownames(apt.dabg))) > #[1] 1381327 > > The APT output is always lower in the PercentPresent. > > Thanks in Advance > > -- output of sessionInfo(): > > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] xps_1.12.1 abind_1.4-0 survival_2.36-14 > [4] affxparser_1.24.0 fastmatch_1.0-4 glmnet_1.7.1 > [7] Matrix_0.999375-50 earth_3.2-3 plotrix_3.4-3 > [10] plotmo_1.3-2 leaps_2.9 rpart_3.1-50 > [13] HDclassif_1.2.1 MASS_7.3-13 randomForest_4.6-6 > [16] e1071_1.6 class_7.3-3 oligo_1.14.0 > [19] oligoClasses_1.14.0 frma_1.3.10 Biobase_2.12.2 > [22] caret_5.15-023 cluster_1.14.0 reshape_0.8.4 > [25] plyr_1.7.1 lattice_0.19-30 matrixStats_0.4.3 > [28] R.methodsS3_1.4.2 abind_1.4-0 foreach_1.4.0 > [31] itertools_0.1-1 iterators_1.0.5 > > loaded via a namespace (and not attached): > [1] affy_1.30.0 affyio_1.20.0 Biostrings_2.20.4 > [4] codetools_0.2-8 DBI_0.2-5 grid_2.13.1 > [7] IRanges_1.10.6 preprocessCore_1.14.0 > > > -- > Sent via the guest posting facility at bioconductor.org. >