Question: beadarray - combing
0
gravatar for Krys Kelly
12.3 years ago by
Krys Kelly270
Krys Kelly270 wrote:
I have been using beadarray to explore 5 Illumina mouse 6 bead chips (i.e. 30 arrays). I would now like to summarise the data using createBeadSummaryData. As the documentation says, this is memory intensive and I do not believe it will be possible to do with with a 32-bit version of R. I am looking into the possibility of being able to use a 64-bit compilation. However, this may take some time. So I was attracted by the help for this function which says: " Objects which are created separately by 'createBeadSummaryData' may be joined by using the cbind function. " I don't know what the trick is, but this doesn't work for me. I just wind up with a 1x2 matrix containing the names of the two bead summary objects I am trying to combine. Here is my code and session information. Thanks for any help. Cheers Krys > BLData39ABC <- readIllumina(arrayNames=c( + "1863191039_A_1", "1863191039_A_2", + "1863191039_B_1", "1863191039_B_2", + "1863191039_C_1", "1863191039_C_2"), + textType=".txt", + backgroundMethod="none", normalizeMethod="none") Found 6 arrays Reading pixels of 1863191039_A_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_A_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_B_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_B_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_C_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_C_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none > BLData39DEF <- readIllumina(arrayNames=c( + "1863191039_D_1", "1863191039_D_2", + "1863191039_E_1", "1863191039_E_2", + "1863191039_F_1", "1863191039_F_2"), + textType=".txt", + backgroundMethod="none", normalizeMethod="none") Found 6 arrays Reading pixels of 1863191039_D_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_D_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_E_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_E_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_F_1_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none Reading pixels of 1863191039_F_2_Grn.tif Calculating background Sharpening Image Calculating foregound Background correcting: method = none > > # Creation of summary data > cat("\nCreating summary data\n") Creating summary data > flush.console() NULL > BSData39ABC <-createBeadSummaryData(BLData39ABC,log=FALSE,n=3,imagesPerArray=2) > BSData39DEF <-createBeadSummaryData(BLData39DEF,log=FALSE,n=3,imagesPerArray=2) > > exprs(BSData39ABC)[1:10, 1:3] 1863191039_A_1 1863191039_B_1 1863191039_C_1 10243 839.6506 845.9098 865.9043 10280 833.1207 834.3494 848.4542 10575 904.3008 910.9755 944.9005 20048 829.4193 827.7526 842.6774 20296 19276.8925 21378.0448 23450.6285 20343 815.6845 817.2897 833.3593 20373 820.7240 820.3355 833.8266 20431 27753.5007 29888.2093 29346.2453 50008 869.3557 1024.7717 1022.3103 50014 800.8334 799.2665 809.7410 > exprs(BSData39DEF)[1:10, 1:3] 1863191039_D_1 1863191039_E_1 1863191039_F_1 10243 839.3879 861.5757 854.2918 10280 831.0985 838.2159 858.3772 10575 896.9414 910.2924 925.6573 20048 833.0732 835.5710 844.9445 20296 21587.3530 19046.5401 22171.7225 20343 833.2653 829.7436 835.0217 20373 828.0081 835.3683 842.4046 20431 32288.4499 28639.5432 31756.6553 50008 1059.4472 1019.7494 1020.6142 50014 807.6089 802.2027 812.7708 > > BSData <- cbind(BSData39ABC, BSData39DEF) > > exprs(BSData)[1:10, 1:3] Error in function (classes, fdef, mtable) : unable to find an inherited method for function "exprs", for signature "matrix" > > BSData BSData39ABC BSData39DEF [1,] ? ? > class(BSData) [1] "matrix" > attributes(BSData) $dim [1] 1 2 $dimnames $dimnames[[1]] NULL $dimnames[[2]] [1] "BSData39ABC" "BSData39DEF" > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] "grid" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM "1.4.0" "1.2.0" "1.2.0" "1.1" "4.08" "0.73" affy affyio geneplotter lattice annotate Biobase "1.14.2" "1.4.1" "1.14.0" "0.15-11" "1.14.1" "1.14.1" limma "2.10.5" > Dr Krystyna A Kelly (Krys) Department of Pathology University of Cambridge, Tennis Court Road, Cambridge CB2 1QP Tel: 01223 333331 and MRC Biostatistics Unit Institute of Public Health, Robinson Way, Cambridge CB2 0SR Tel: 01223 767408 Email: kak28 at cam.ac.uk
ADD COMMENTlink modified 12.3 years ago by Mark Dunning320 • written 12.3 years ago by Krys Kelly270
Answer: beadarray - combing
0
gravatar for Mark Dunning
12.3 years ago by
Mark Dunning320
Mark Dunning320 wrote:
Hi Krys, Sorry, it seems that the manual page for createBeadSummaryData is either out of date or contains a typo. The function we use to join summarised data is actually called combine so you would use BSData = combine(BSData39ABC, BSData39DEF) to get the required result. Hope this helps and thanks for bringing it to my attention Regards, Mark On 8 Aug 2007, at 17:07, Krys Kelly wrote: > I have been using beadarray to explore 5 Illumina mouse 6 bead > chips (i.e. > 30 arrays). I would now like to summarise the data using > createBeadSummaryData. As the documentation says, this is memory > intensive > and I do not believe it will be possible to do with with a 32-bit > version of > R. I am looking into the possibility of being able to use a 64-bit > compilation. However, this may take some time. > > So I was attracted by the help for this function which says: > > " Objects which are created separately by 'createBeadSummaryData' > may be > joined by using the cbind function. " > > I don't know what the trick is, but this doesn't work for me. I > just wind > up with a 1x2 matrix containing the names of the two bead summary > objects I > am trying to combine. > > Here is my code and session information. > > Thanks for any help. > > Cheers > > Krys > > >> BLData39ABC <- readIllumina(arrayNames=c( > + "1863191039_A_1", "1863191039_A_2", > + "1863191039_B_1", "1863191039_B_2", > + "1863191039_C_1", "1863191039_C_2"), > + textType=".txt", > + backgroundMethod="none", > normalizeMethod="none") > Found 6 arrays > Reading pixels of 1863191039_A_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_A_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_B_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_B_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_C_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_C_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > >> BLData39DEF <- readIllumina(arrayNames=c( > + "1863191039_D_1", "1863191039_D_2", > + "1863191039_E_1", "1863191039_E_2", > + "1863191039_F_1", "1863191039_F_2"), > + textType=".txt", > + backgroundMethod="none", > normalizeMethod="none") > Found 6 arrays > Reading pixels of 1863191039_D_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_D_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_E_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_E_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_F_1_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none > Reading pixels of 1863191039_F_2_Grn.tif > Calculating background > Sharpening Image > Calculating foregound > Background correcting: method = none >> >> # Creation of summary data >> cat("\nCreating summary data\n") > > Creating summary data >> flush.console() > NULL >> BSData39ABC > <-createBeadSummaryData(BLData39ABC,log=FALSE,n=3,imagesPerArray=2) >> BSData39DEF > <-createBeadSummaryData(BLData39DEF,log=FALSE,n=3,imagesPerArray=2) >> >> exprs(BSData39ABC)[1:10, 1:3] > 1863191039_A_1 1863191039_B_1 1863191039_C_1 > 10243 839.6506 845.9098 865.9043 > 10280 833.1207 834.3494 848.4542 > 10575 904.3008 910.9755 944.9005 > 20048 829.4193 827.7526 842.6774 > 20296 19276.8925 21378.0448 23450.6285 > 20343 815.6845 817.2897 833.3593 > 20373 820.7240 820.3355 833.8266 > 20431 27753.5007 29888.2093 29346.2453 > 50008 869.3557 1024.7717 1022.3103 > 50014 800.8334 799.2665 809.7410 >> exprs(BSData39DEF)[1:10, 1:3] > 1863191039_D_1 1863191039_E_1 1863191039_F_1 > 10243 839.3879 861.5757 854.2918 > 10280 831.0985 838.2159 858.3772 > 10575 896.9414 910.2924 925.6573 > 20048 833.0732 835.5710 844.9445 > 20296 21587.3530 19046.5401 22171.7225 > 20343 833.2653 829.7436 835.0217 > 20373 828.0081 835.3683 842.4046 > 20431 32288.4499 28639.5432 31756.6553 > 50008 1059.4472 1019.7494 1020.6142 > 50014 807.6089 802.2027 812.7708 >> >> BSData <- cbind(BSData39ABC, BSData39DEF) >> >> exprs(BSData)[1:10, 1:3] > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "exprs", for > signature "matrix" >> >> BSData > BSData39ABC BSData39DEF > [1,] ? ? > >> class(BSData) > [1] "matrix" > >> attributes(BSData) > $dim > [1] 1 2 > > $dimnames > $dimnames[[1]] > NULL > > $dimnames[[2]] > [1] "BSData39ABC" "BSData39DEF" > > >> sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "grid" "tools" "stats" "graphics" "grDevices" > "utils" > [7] "datasets" "methods" "base" > > other attached packages: > beadarray beadarraySNP quantsmooth lodplot quantreg > SparseM > "1.4.0" "1.2.0" "1.2.0" "1.1" "4.08" > "0.73" > affy affyio geneplotter lattice annotate > Biobase > "1.14.2" "1.4.1" "1.14.0" "0.15-11" "1.14.1" > "1.14.1" > limma > "2.10.5" >> > > > > Dr Krystyna A Kelly (Krys) > > Department of Pathology > University of Cambridge, Tennis Court Road, Cambridge CB2 1QP > Tel: 01223 333331 > > and > > MRC Biostatistics Unit > Institute of Public Health, Robinson Way, Cambridge CB2 0SR > Tel: 01223 767408 > > Email: kak28 at cam.ac.uk > > _______________________________________________ > 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
ADD COMMENTlink written 12.3 years ago by Mark Dunning320
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