Hello, to get the location of perfect matches from an AffyBatch I use the function pmindex(). If I send my AffyBatch to a slave and use the pmindex() function at the slave I get an other result than using the function at the master node. Attached you can find some simple testcode and the sessionInfo plot. You can see, that the same annotation package will be used at the master and at the slaves. Therefore there should be the same index structure. But there is a difference! Any ideas for solutions? Best regards Markus ################## library(snow) c1<- makeCluster(1) library(affy) library(affydata) data(Dilution) indexMaster <- pmindex(Dilution) indexSlave <- clusterCall(c1, function(x) { library(affy); pmindex(x)}, Dilution) # Returns a LIST! all.equal(indexMaster, indexSlave[[1]]) [1] "Names: 40 string mismatches" [2] "Component 12586: Numeric: lengths (69, 20) differ" [3] "Component 12587: Mean relative difference: 1.345755" [4] "Component 12588: Mean relative difference: 0.5620998" [5] "Component 12589: Mean relative difference: 0.6626076" [6] "Component 12590: Mean relative difference: 0.487681" [7] "Component 12591: Mean relative difference: 0.4553995" [8] "Component 12592: Mean relative difference: 0.4263176" [9] "Component 12593: Mean relative difference: 0.5712674" [10] "Component 12594: Mean relative difference: 0.9872221" [11] "Component 12595: Mean relative difference: 0.6511257" [12] "Component 12596: Mean relative difference: 1.118144" [13] "Component 12597: Mean relative difference: 0.7570665" [14] "Component 12598: Mean relative difference: 0.6555009" [15] "Component 12599: Mean relative difference: 0.8429751" [16] "Component 12600: Mean relative difference: 0.8220698" [17] "Component 12601: Mean relative difference: 0.5806326" [18] "Component 12602: Mean relative difference: 0.9459446" [19] "Component 12603: Mean relative difference: 0.005017876" [20] "Component 12604: Mean relative difference: 0.002521591" [21] "Component 12605: Mean relative difference: 17.80169" [22] "Component 12606: Mean relative difference: 0.6895796" [23] "Component 12607: Mean relative difference: 1.435084" [24] "Component 12608: Mean relative difference: 0.9511139" [25] "Component 12609: Mean relative difference: 0.004859382" [26] "Component 12610: Mean relative difference: 0.002441555" [27] "Component 12611: Mean relative difference: 0.004895062" [28] "Component 12612: Mean relative difference: 0.02192048" [29] "Component 12613: Mean relative difference: 0.00498039" [30] "Component 12614: Mean relative difference: 0.002502659" [31] "Component 12615: Mean relative difference: 0.009985646" [32] "Component 12616: Mean relative difference: 0.004943459" [33] "Component 12617: Mean relative difference: 0.002484009" [34] "Component 12618: Mean relative difference: 0.009911417" [35] "Component 12619: Mean relative difference: 0.004907072" [36] "Component 12620: Mean relative difference: 0.002465635" [37] "Component 12621: Mean relative difference: 0.01475742" [38] "Component 12622: Mean relative difference: 0.002423802" [39] "Component 12623: Mean relative difference: 0.01259747" [40] "Component 12624: Mean relative difference: 0.01005289" [41] "Component 12625: Numeric: lengths (20, 69) differ" indexMaster[12586] $`AFFX-hum_alu_at` [1] 250676 375731 211930 327074 352651 352650 43467 159539 159540 171051 [11] 231270 102022 263133 140413 278581 178848 178847 214557 191494 191495 [21] 38016 228673 277142 275902 114699 215783 77671 21489 21490 267349 [31] 276339 257960 305449 305450 279710 22853 22854 163552 336192 339896 [41] 35483 43466 43465 171053 171052 102024 102023 263134 278582 278583 [51] 277394 373143 214556 58516 58515 270948 249046 318231 126406 57395 [61] 247739 154374 154375 154376 144365 254115 254116 337311 337310 indexSlave[[1]][12586] $`AFFX-HUMGAPDH/M33197_3_at` [1] 121056 36917 261006 35492 126329 176294 141533 368370 155742 84276 [11] 137751 66002 4753 26735 71484 102044 214559 25066 127497 114997 sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE .UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu95av2cdf_2.0.0 affydata_1.11.3 affy_1.16.0 [4] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 [7] Rmpi_0.5-6 snow_0.2-9 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 clusterEvalQ(c1, sessionInfo()) [[1]] R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu95av2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 [4] affyio_1.6.1 Biobase_1.16.1 snow_0.2-9 [7] Rmpi_0.5-6 stopCluster(c1) -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

Hi Markus -- pmindex eventually calls ls() on the cdf environment. ls() gets all the probe names and then sorts them. This is where I bet your problem occurs -- your master and worker nodes have different locales, (de_DE.UTF-8 vs C) and so sort the probe names differently. Perhaps you're getting the same answers, just in the different order? Try sorting the results by probe name before all.equal. Martin Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de=""> writes: > Hello, > > to get the location of perfect matches from an AffyBatch I use the > function pmindex(). > If I send my AffyBatch to a slave and use the pmindex() function at > the slave I get an other result than using the function at the master > node. > > Attached you can find some simple testcode and the sessionInfo plot. > You can see, that the same annotation package will be used at the > master and at the slaves. Therefore there should be the same index > structure. But there is a difference! > > Any ideas for solutions? > > Best regards > Markus > > ################## > library(snow) > c1<- makeCluster(1) > > library(affy) > library(affydata) > data(Dilution) > > indexMaster <- pmindex(Dilution) > indexSlave <- clusterCall(c1, function(x) { library(affy); > pmindex(x)}, Dilution) # Returns a LIST! > > all.equal(indexMaster, indexSlave[[1]]) > [1] "Names: 40 string mismatches" [2] > "Component 12586: Numeric: lengths (69, 20) differ" [3] "Component > 12587: Mean relative difference: 1.345755" [4] "Component 12588: > Mean relative difference: 0.5620998" [5] "Component 12589: Mean > relative difference: 0.6626076" [6] "Component 12590: Mean relative > difference: 0.487681" [7] "Component 12591: Mean relative > difference: 0.4553995" [8] "Component 12592: Mean relative > difference: 0.4263176" [9] "Component 12593: Mean relative > difference: 0.5712674" [10] "Component 12594: Mean relative > difference: 0.9872221" [11] "Component 12595: Mean relative > difference: 0.6511257" [12] "Component 12596: Mean relative > difference: 1.118144" [13] "Component 12597: Mean relative > difference: 0.7570665" [14] "Component 12598: Mean relative > difference: 0.6555009" [15] "Component 12599: Mean relative > difference: 0.8429751" [16] "Component 12600: Mean relative > difference: 0.8220698" [17] "Component 12601: Mean relative > difference: 0.5806326" [18] "Component 12602: Mean relative > difference: 0.9459446" [19] "Component 12603: Mean relative > difference: 0.005017876" > [20] "Component 12604: Mean relative difference: 0.002521591" > [21] "Component 12605: Mean relative difference: 17.80169" [22] > "Component 12606: Mean relative difference: 0.6895796" [23] > "Component 12607: Mean relative difference: 1.435084" [24] > "Component 12608: Mean relative difference: 0.9511139" [25] > "Component 12609: Mean relative difference: 0.004859382" > [26] "Component 12610: Mean relative difference: 0.002441555" > [27] "Component 12611: Mean relative difference: 0.004895062" > [28] "Component 12612: Mean relative difference: 0.02192048" > [29] "Component 12613: Mean relative difference: 0.00498039" > [30] "Component 12614: Mean relative difference: 0.002502659" > [31] "Component 12615: Mean relative difference: 0.009985646" > [32] "Component 12616: Mean relative difference: 0.004943459" > [33] "Component 12617: Mean relative difference: 0.002484009" > [34] "Component 12618: Mean relative difference: 0.009911417" > [35] "Component 12619: Mean relative difference: 0.004907072" > [36] "Component 12620: Mean relative difference: 0.002465635" > [37] "Component 12621: Mean relative difference: 0.01475742" > [38] "Component 12622: Mean relative difference: 0.002423802" > [39] "Component 12623: Mean relative difference: 0.01259747" > [40] "Component 12624: Mean relative difference: 0.01005289" > [41] "Component 12625: Numeric: lengths (20, 69) differ" > > indexMaster[12586] > $`AFFX-hum_alu_at` > [1] 250676 375731 211930 327074 352651 352650 43467 159539 159540 171051 > [11] 231270 102022 263133 140413 278581 178848 178847 214557 191494 191495 > [21] 38016 228673 277142 275902 114699 215783 77671 21489 21490 267349 > [31] 276339 257960 305449 305450 279710 22853 22854 163552 336192 339896 > [41] 35483 43466 43465 171053 171052 102024 102023 263134 278582 278583 > [51] 277394 373143 214556 58516 58515 270948 249046 318231 126406 57395 > [61] 247739 154374 154375 154376 144365 254115 254116 337311 337310 > > indexSlave[[1]][12586] > $`AFFX-HUMGAPDH/M33197_3_at` > [1] 121056 36917 261006 35492 126329 176294 141533 368370 155742 84276 > [11] 137751 66002 4753 26735 71484 102044 214559 25066 127497 114997 > > sessionInfo() > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF -8;LC_IDENTIFICATION=C > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods [8] base other attached packages: > [1] hgu95av2cdf_2.0.0 affydata_1.11.3 affy_1.16.0 [4] > preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 [7] > Rmpi_0.5-6 snow_0.2-9 loaded via a namespace (and > not attached): > [1] rcompgen_0.1-15 > > > clusterEvalQ(c1, sessionInfo()) > [[1]] > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > locale: > C > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods [8] base other attached packages: > [1] hgu95av2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 > [4] affyio_1.6.1 Biobase_1.16.1 snow_0.2-9 [7] > Rmpi_0.5-6 > > > stopCluster(c1) > > > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universit?t M?nchen > IBE - Institut f?r medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] > ibe.med.uni-muenchen.de > Tel: +49 (089) 7095 - 4599 > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Hi Markus I just tried this myself but didn't see the problems you did. Not sure exactly why you're seeing what you do, but I note that you have Rmpi_0.5-6, whereas I believe the current release version is Rmpi_0.5-5. I'd suggest installing R 2.7.0 and using biocLite to install packages, then try again. Below is the output I got with your script - hope this helps! Best wishes Richard > library(snow) > c1<- makeCluster(1) Loading required package: Rmpi 1 slaves are spawned successfully. 0 failed. > > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore > library(affydata) > data(Dilution) > > indexMaster <- pmindex(Dilution) > indexSlave <- clusterCall(c1, function(x) { library(affy); pmindex(x)}, Dilution) # Returns a LIST! > > all.equal(indexMaster, indexSlave[[1]]) [1] TRUE > > indexMaster[12586] $`AFFX-HUMGAPDH/M33197_3_at` [1] 121056 36917 261006 35492 126329 176294 141533 368370 155742 84276 137751 66002 4753 26735 71484 102044 214559 25066 127497 114997 > indexSlave[[1]][12586] $`AFFX-HUMGAPDH/M33197_3_at` [1] 121056 36917 261006 35492 126329 176294 141533 368370 155742 84276 137751 66002 4753 26735 71484 102044 214559 25066 127497 114997 > > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices datasets utils methods base other attached packages: [1] hgu95av2cdf_2.2.0 affydata_1.11.3 affy_1.18.0 preprocessCore_1.1.9 affyio_1.7.17 Biobase_2.0.0 Rmpi_0.5-5 [8] snow_0.2-9 > > clusterEvalQ(c1, sessionInfo()) [[1]] R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2cdf_2.2.0 affy_1.18.0 preprocessCore_1.1.9 affyio_1.7.17 Biobase_2.0.0 snow_0.2-9 Rmpi_0.5-5 Markus Schmidberger wrote: > Hello, > > to get the location of perfect matches from an AffyBatch I use the > function pmindex(). > If I send my AffyBatch to a slave and use the pmindex() function at the > slave I get an other result than using the function at the master node. > > Attached you can find some simple testcode and the sessionInfo plot. > You can see, that the same annotation package will be used at the master > and at the slaves. Therefore there should be the same index structure. > But there is a difference! > > Any ideas for solutions? > > Best regards > Markus > > ################## > library(snow) > c1<- makeCluster(1) > > library(affy) > library(affydata) > data(Dilution) > > indexMaster <- pmindex(Dilution) > indexSlave <- clusterCall(c1, function(x) { library(affy); pmindex(x)}, > Dilution) # Returns a LIST! > > all.equal(indexMaster, indexSlave[[1]]) > [1] "Names: 40 string mismatches" [2] > "Component 12586: Numeric: lengths (69, 20) differ" [3] "Component > 12587: Mean relative difference: 1.345755" [4] "Component 12588: Mean > relative difference: 0.5620998" [5] "Component 12589: Mean relative > difference: 0.6626076" [6] "Component 12590: Mean relative difference: > 0.487681" [7] "Component 12591: Mean relative difference: 0.4553995" > [8] "Component 12592: Mean relative difference: 0.4263176" [9] > "Component 12593: Mean relative difference: 0.5712674" [10] "Component > 12594: Mean relative difference: 0.9872221" [11] "Component 12595: Mean > relative difference: 0.6511257" [12] "Component 12596: Mean relative > difference: 1.118144" [13] "Component 12597: Mean relative difference: > 0.7570665" [14] "Component 12598: Mean relative difference: 0.6555009" > [15] "Component 12599: Mean relative difference: 0.8429751" [16] > "Component 12600: Mean relative difference: 0.8220698" [17] "Component > 12601: Mean relative difference: 0.5806326" [18] "Component 12602: Mean > relative difference: 0.9459446" [19] "Component 12603: Mean relative > difference: 0.005017876" > [20] "Component 12604: Mean relative difference: 0.002521591" > [21] "Component 12605: Mean relative difference: 17.80169" [22] > "Component 12606: Mean relative difference: 0.6895796" [23] "Component > 12607: Mean relative difference: 1.435084" [24] "Component 12608: Mean > relative difference: 0.9511139" [25] "Component 12609: Mean relative > difference: 0.004859382" > [26] "Component 12610: Mean relative difference: 0.002441555" > [27] "Component 12611: Mean relative difference: 0.004895062" > [28] "Component 12612: Mean relative difference: 0.02192048" > [29] "Component 12613: Mean relative difference: 0.00498039" > [30] "Component 12614: Mean relative difference: 0.002502659" > [31] "Component 12615: Mean relative difference: 0.009985646" > [32] "Component 12616: Mean relative difference: 0.004943459" > [33] "Component 12617: Mean relative difference: 0.002484009" > [34] "Component 12618: Mean relative difference: 0.009911417" > [35] "Component 12619: Mean relative difference: 0.004907072" > [36] "Component 12620: Mean relative difference: 0.002465635" > [37] "Component 12621: Mean relative difference: 0.01475742" > [38] "Component 12622: Mean relative difference: 0.002423802" > [39] "Component 12623: Mean relative difference: 0.01259747" > [40] "Component 12624: Mean relative difference: 0.01005289" > [41] "Component 12625: Numeric: lengths (20, 69) differ" > > indexMaster[12586] > $`AFFX-hum_alu_at` > [1] 250676 375731 211930 327074 352651 352650 43467 159539 159540 171051 > [11] 231270 102022 263133 140413 278581 178848 178847 214557 191494 191495 > [21] 38016 228673 277142 275902 114699 215783 77671 21489 21490 267349 > [31] 276339 257960 305449 305450 279710 22853 22854 163552 336192 339896 > [41] 35483 43466 43465 171053 171052 102024 102023 263134 278582 278583 > [51] 277394 373143 214556 58516 58515 270948 249046 318231 126406 57395 > [61] 247739 154374 154375 154376 144365 254115 254116 337311 337310 > > indexSlave[[1]][12586] > $`AFFX-HUMGAPDH/M33197_3_at` > [1] 121056 36917 261006 35492 126329 176294 141533 368370 155742 84276 > [11] 137751 66002 4753 26735 71484 102044 214559 25066 127497 114997 > > sessionInfo() > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base other attached packages: > [1] hgu95av2cdf_2.0.0 affydata_1.11.3 affy_1.16.0 [4] > preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 [7] > Rmpi_0.5-6 snow_0.2-9 loaded via a namespace (and not > attached): > [1] rcompgen_0.1-15 > > > clusterEvalQ(c1, sessionInfo()) > [[1]] > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > locale: > C > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base other attached packages: > [1] hgu95av2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 > [4] affyio_1.6.1 Biobase_1.16.1 snow_0.2-9 [7] > Rmpi_0.5-6 > > stopCluster(c1) > > > -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204