combineBeadLevelLists() in Bioconductor 2.8 beadarray
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@alex-gutteridge-2935
Last seen 10.2 years ago
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Hi, Older versions of beadarray have a combineBeadLevelList() for combining bead level data lists read from two different Illumina chips into one list. In the latest beadarray this seems to have been removed, but I can't find anything in the documentation describing the correct way to do this with the new beadLevelData class. Am I missing something obvious or is this no longer supported? > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-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] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] reshape_0.8.3 plyr_1.2.1 nlme_3.1-97 [4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 RSQLite_0.9-3 [7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.0 [10] limma_3.6.6 latticeExtra_0.6-14 RColorBrewer_1.0-2 [13] lattice_0.19-13 contrast_0.13 Design_2.3-0 [16] Hmisc_3.8-3 survival_2.36-1 Cairo_1.4-5 [19] beadarray_2.0.2 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 [4] cluster_1.13.2 grid_2.12.0 hdrcde_2.14 [7] KernSmooth_2.23-4 MASS_7.3-8 Matrix_0.999375-44 [10] methylumi_1.4.0 mgcv_1.7-1 preprocessCore_1.12.0 [13] tcltk_2.12.0 tools_2.12.0 xtable_1.5-6 -- Alex Gutteridge
beadarray beadarray • 1.1k views
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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 21 months ago
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Hi Alex, The functionality still exists in beadarray, but can be called using the generic 'combine' rather than combineBeadLevelLists. Best wishes, Mark On Tue, Dec 7, 2010 at 10:20 AM, Alex Gutteridge <alexg at="" ruggedtextile.com=""> wrote: > Hi, > > Older versions of beadarray have a combineBeadLevelList() for combining > bead level data lists read from two different Illumina chips into one list. > In the latest beadarray this seems to have been removed, but I can't find > anything in the documentation describing the correct way to do this with > the new beadLevelData class. Am I missing something obvious or is this no > longer supported? > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-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] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] reshape_0.8.3 ? ? ? ? ?plyr_1.2.1 ? ? ? ? ? ? nlme_3.1-97 > ?[4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 ? ? RSQLite_0.9-3 > ?[7] DBI_0.2-5 ? ? ? ? ? ? ?AnnotationDbi_1.12.0 ? lumi_2.2.0 > [10] limma_3.6.6 ? ? ? ? ? ?latticeExtra_0.6-14 ? ?RColorBrewer_1.0-2 > [13] lattice_0.19-13 ? ? ? ?contrast_0.13 ? ? ? ? ?Design_2.3-0 > [16] Hmisc_3.8-3 ? ? ? ? ? ?survival_2.36-1 ? ? ? ?Cairo_1.4-5 > [19] beadarray_2.0.2 ? ? ? ?Biobase_2.10.0 > > loaded via a namespace (and not attached): > ?[1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.0 > ?[4] cluster_1.13.2 ? ? ? ?grid_2.12.0 ? ? ? ? ? hdrcde_2.14 > ?[7] KernSmooth_2.23-4 ? ? MASS_7.3-8 ? ? ? ? ? ?Matrix_0.999375-44 > [10] methylumi_1.4.0 ? ? ? mgcv_1.7-1 ? ? ? ? ? ?preprocessCore_1.12.0 > [13] tcltk_2.12.0 ? ? ? ? ?tools_2.12.0 ? ? ? ? ?xtable_1.5-6 > > -- > Alex Gutteridge > > _______________________________________________ > 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 >
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Hi Mark, Sorry, maybe I'm being dim, but how do you call combine() correctly? > dir1 <- "/5168671015" > iBatch1 <- readIllumina(dir = paste(".", dir1, sep = ""), + useImages = FALSE, + metricsFile = "Metrics.txt", + illuminaAnnotation="Humanv4") Processing section 5168671015_A_1 Processing section 5168671015_B_1 Processing section 5168671015_C_1 Processing section 5168671015_D_1 Processing section 5168671015_E_1 Processing section 5168671015_F_1 Processing section 5168671015_G_1 Processing section 5168671015_H_1 Processing section 5168671015_I_1 Processing section 5168671015_J_1 Processing section 5168671015_K_1 Processing section 5168671015_L_1 > dir2 <- "/5168671022" > iBatch2 <- readIllumina(dir = paste(".", dir2, sep = ""), + useImages = FALSE, + metricsFile = "Metrics.txt", + illuminaAnnotation="Humanv4") Processing section 5168671022_A_1 Processing section 5168671022_B_1 Processing section 5168671022_C_1 Processing section 5168671022_D_1 Processing section 5168671022_E_1 Processing section 5168671022_F_1 Processing section 5168671022_G_1 Processing section 5168671022_H_1 Processing section 5168671022_I_1 Processing section 5168671022_J_1 Processing section 5168671022_K_1 Processing section 5168671022_L_1 > iBatch = combine(iBatch1,iBatch2) Error in combine(iBatch1, iBatch2) : unable to combine these objects > class(iBatch1) [1] "beadLevelData" attr(,"package") [1] "beadarray" > class(iBatch2) [1] "beadLevelData" attr(,"package") [1] "beadarray" On Tue, 7 Dec 2010 10:46:21 +0000, Mark Dunning <mark.dunning at="" gmail.com=""> wrote: > Hi Alex, > > The functionality still exists in beadarray, but can be called using > the generic 'combine' rather than combineBeadLevelLists. > > Best wishes, > > Mark > > On Tue, Dec 7, 2010 at 10:20 AM, Alex Gutteridge > <alexg at="" ruggedtextile.com=""> wrote: >> Hi, >> >> Older versions of beadarray have a combineBeadLevelList() for combining >> bead level data lists read from two different Illumina chips into one >> list. >> In the latest beadarray this seems to have been removed, but I can't find >> anything in the documentation describing the correct way to do this with >> the new beadLevelData class. Am I missing something obvious or is this no >> longer supported? >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-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] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> [8] base >> >> other attached packages: >> ?[1] reshape_0.8.3 ? ? ? ? ?plyr_1.2.1 ? ? ? ? ? ? nlme_3.1-97 >> ?[4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 ? ? RSQLite_0.9-3 >> ?[7] DBI_0.2-5 ? ? ? ? ? ? ?AnnotationDbi_1.12.0 ? lumi_2.2.0 >> [10] limma_3.6.6 ? ? ? ? ? ?latticeExtra_0.6-14 ? ?RColorBrewer_1.0-2 >> [13] lattice_0.19-13 ? ? ? ?contrast_0.13 ? ? ? ? ?Design_2.3-0 >> [16] Hmisc_3.8-3 ? ? ? ? ? ?survival_2.36-1 ? ? ? ?Cairo_1.4-5 >> [19] beadarray_2.0.2 ? ? ? ?Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> ?[1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.0 >> ?[4] cluster_1.13.2 ? ? ? ?grid_2.12.0 ? ? ? ? ? hdrcde_2.14 >> ?[7] KernSmooth_2.23-4 ? ? MASS_7.3-8 ? ? ? ? ? ?Matrix_0.999375-44 >> [10] methylumi_1.4.0 ? ? ? mgcv_1.7-1 ? ? ? ? ? ?preprocessCore_1.12.0 >> [13] tcltk_2.12.0 ? ? ? ? ?tools_2.12.0 ? ? ? ? ?xtable_1.5-6 >> >> -- >> Alex Gutteridge >> >> _______________________________________________ >> 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 >> -- Alex Gutteridge
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Hi Alex, No, you're correct. That should be how to combine two object and it's not immediately clear what the problem might be. If you run >showMethods("combine") Do you see a method listed that combines beadLevelData objects? Do iBatch1 and iBatch2 look like valid beadLevelData objects? >iBatch1 >iBatch2 Mark On Tue, Dec 7, 2010 at 11:32 AM, Alex Gutteridge <alexg at="" ruggedtextile.com=""> wrote: > Hi Mark, > > Sorry, maybe I'm being dim, but how do you call combine() correctly? > >> ? ? dir1 ? ? <- "/5168671015" >> ? ? iBatch1 ?<- readIllumina(dir = paste(".", dir1, sep = ""), > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?useImages = FALSE, > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?metricsFile = "Metrics.txt", > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?illuminaAnnotation="Humanv4") > Processing section 5168671015_A_1 > Processing section 5168671015_B_1 > Processing section 5168671015_C_1 > Processing section 5168671015_D_1 > Processing section 5168671015_E_1 > Processing section 5168671015_F_1 > Processing section 5168671015_G_1 > Processing section 5168671015_H_1 > Processing section 5168671015_I_1 > Processing section 5168671015_J_1 > Processing section 5168671015_K_1 > Processing section 5168671015_L_1 >> ? ? dir2 ? ? <- "/5168671022" >> ? ? iBatch2 ?<- readIllumina(dir = paste(".", dir2, sep = ""), > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?useImages = FALSE, > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?metricsFile = "Metrics.txt", > + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?illuminaAnnotation="Humanv4") > Processing section 5168671022_A_1 > Processing section 5168671022_B_1 > Processing section 5168671022_C_1 > Processing section 5168671022_D_1 > Processing section 5168671022_E_1 > Processing section 5168671022_F_1 > Processing section 5168671022_G_1 > Processing section 5168671022_H_1 > Processing section 5168671022_I_1 > Processing section 5168671022_J_1 > Processing section 5168671022_K_1 > Processing section 5168671022_L_1 >> iBatch = combine(iBatch1,iBatch2) > Error in combine(iBatch1, iBatch2) : unable to combine these objects >> class(iBatch1) > [1] "beadLevelData" > attr(,"package") > [1] "beadarray" >> class(iBatch2) > [1] "beadLevelData" > attr(,"package") > [1] "beadarray" > > On Tue, 7 Dec 2010 10:46:21 +0000, Mark Dunning <mark.dunning at="" gmail.com=""> > wrote: >> Hi Alex, >> >> The functionality still exists in beadarray, but can be called using >> the generic 'combine' rather than combineBeadLevelLists. >> >> Best wishes, >> >> Mark >> >> On Tue, Dec 7, 2010 at 10:20 AM, Alex Gutteridge >> <alexg at="" ruggedtextile.com=""> wrote: >>> Hi, >>> >>> Older versions of beadarray have a combineBeadLevelList() for combining >>> bead level data lists read from two different Illumina chips into one >>> list. >>> In the latest beadarray this seems to have been removed, but I can't > find >>> anything in the documentation describing the correct way to do this > with >>> the new beadLevelData class. Am I missing something obvious or is this > no >>> longer supported? >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-unknown-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] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods >>> [8] base >>> >>> other attached packages: >>> ?[1] reshape_0.8.3 ? ? ? ? ?plyr_1.2.1 ? ? ? ? ? ? nlme_3.1-97 >>> ?[4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 ? ? RSQLite_0.9-3 >>> ?[7] DBI_0.2-5 ? ? ? ? ? ? ?AnnotationDbi_1.12.0 ? lumi_2.2.0 >>> [10] limma_3.6.6 ? ? ? ? ? ?latticeExtra_0.6-14 ? ?RColorBrewer_1.0-2 >>> [13] lattice_0.19-13 ? ? ? ?contrast_0.13 ? ? ? ? ?Design_2.3-0 >>> [16] Hmisc_3.8-3 ? ? ? ? ? ?survival_2.36-1 ? ? ? ?Cairo_1.4-5 >>> [19] beadarray_2.0.2 ? ? ? ?Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> ?[1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.0 >>> ?[4] cluster_1.13.2 ? ? ? ?grid_2.12.0 ? ? ? ? ? hdrcde_2.14 >>> ?[7] KernSmooth_2.23-4 ? ? MASS_7.3-8 ? ? ? ? ? ?Matrix_0.999375-44 >>> [10] methylumi_1.4.0 ? ? ? mgcv_1.7-1 ? ? ? ? ? ?preprocessCore_1.12.0 >>> [13] tcltk_2.12.0 ? ? ? ? ?tools_2.12.0 ? ? ? ? ?xtable_1.5-6 >>> >>> -- >>> Alex Gutteridge >>> >>> _______________________________________________ >>> 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 >>> > > -- > Alex Gutteridge >
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Everything looks OK - I see the beadLevelData combine() method. Can you see anything obviously wrong with the beadLevelData objects themselves? The only thing that I can see is that the Metrics are all NA. > class(iBatch1) [1] "beadLevelData" attr(,"package") [1] "beadarray" > class(iBatch2) [1] "beadLevelData" attr(,"package") [1] "beadarray" > showMethods("combine") Function: combine (package Biobase) x="AnnotatedDataFrame", y="AnnotatedDataFrame" x="ANY", y="missing" x="AssayData", y="AssayData" x="beadLevelData", y="beadLevelData" x="data.frame", y="data.frame" x="eSet", y="eSet" x="ExpressionSetIllumina", y="ExpressionSetIllumina" x="ExpressionSet", y="LumiBatch" x="LumiBatch", y="ExpressionSet" x="LumiBatch", y="LumiBatch" x="matrix", y="matrix" x="MethyLumiSet", y="MethyLumiSet" x="MIAME", y="MIAME" > iBatch1 Experiment information $sdfFile [1] "/data1/Projects/Pancreas/inVivo/5168671015/5168671015.sdf" $platformClass [1] "Slide" $annotation [1] "Humanv4" Targets directory sectionName textFile 1 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_A_1 5168671015_A_1.txt 2 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_B_1 5168671015_B_1.txt 3 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_C_1 5168671015_C_1.txt 4 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_D_1 5168671015_D_1.txt 5 /data1/Projects/Pancreas/inVivo/5168671015 5168671015_E_1 5168671015_E_1.txt greenImage 1 5168671015_A_1_Grn.tif 2 5168671015_B_1_Grn.tif 3 5168671015_C_1_Grn.tif 4 5168671015_D_1_Grn.tif 5 5168671015_E_1_Grn.tif .. 2 more columns of data Metrics Date Beadchip Section FocusGrn NA <na> NA <na> NA NA.1 <na> NA <na> NA NA.2 <na> NA <na> NA NA.3 <na> NA <na> NA NA.4 <na> NA <na> NA .. 7 more columns of data SampleGroup [1] A B C D E Levels: A B C D E F G H I J K L numBeads [1] 1018509 1014208 1029054 1015868 1016981 Array information Raw data from section 5168671015_A_1 ProbeID GrnX GrnY Grn [1,] 10008 1640.5000 24330.480 1021 [2,] 10008 302.5283 24325.500 613 [3,] 10008 540.5187 19041.480 640 [4,] 10008 1219.5060 1755.484 968 [5,] 10008 1031.5120 20808.510 1217 ... 1018504 more rows of data ... data for 11 more array/s > iBatch2 Experiment information $sdfFile [1] "/data1/Projects/Pancreas/inVivo/5168671022/5168671022.sdf" $platformClass [1] "Slide" $annotation [1] "Humanv4" Targets directory sectionName textFile 1 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_A_1 5168671022_A_1.txt 2 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_B_1 5168671022_B_1.txt 3 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_C_1 5168671022_C_1.txt 4 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_D_1 5168671022_D_1.txt 5 /data1/Projects/Pancreas/inVivo/5168671022 5168671022_E_1 5168671022_E_1.txt greenImage 1 5168671022_A_1_Grn.tif 2 5168671022_B_1_Grn.tif 3 5168671022_C_1_Grn.tif 4 5168671022_D_1_Grn.tif 5 5168671022_E_1_Grn.tif .. 2 more columns of data Metrics Date Beadchip Section FocusGrn NA <na> NA <na> NA NA.1 <na> NA <na> NA NA.2 <na> NA <na> NA NA.3 <na> NA <na> NA NA.4 <na> NA <na> NA .. 7 more columns of data SampleGroup [1] A B C D E Levels: A B C D E F G H I J K L numBeads [1] 1042066 1036063 1050477 1047443 1054511 Array information Raw data from section 5168671022_A_1 ProbeID GrnX GrnY Grn [1,] 10008 1703.4920 658.5403 1029 [2,] 10008 1103.4780 8908.4650 650 [3,] 10008 1938.5220 14068.5000 699 [4,] 10008 1781.4860 6699.4960 904 [5,] 10008 798.4817 1983.4770 1242 ... 1042061 more rows of data ... data for 11 more array/s On Tue, 7 Dec 2010 13:14:57 +0000, Mark Dunning <mark.dunning at="" gmail.com=""> wrote: > Hi Alex, > > No, you're correct. That should be how to combine two object and it's > not immediately clear what the problem might be. If you run > >>showMethods("combine") > > Do you see a method listed that combines beadLevelData objects? Do > iBatch1 and iBatch2 look like valid beadLevelData objects? > >>iBatch1 >>iBatch2 > > Mark > > On Tue, Dec 7, 2010 at 11:32 AM, Alex Gutteridge > <alexg at="" ruggedtextile.com=""> wrote: >> Hi Mark, >> >> Sorry, maybe I'm being dim, but how do you call combine() correctly? >> >>> ? ? dir1 ? ? <- "/5168671015" >>> ? ? iBatch1 ?<- readIllumina(dir = paste(".", dir1, sep = ""), >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?useImages = FALSE, >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?metricsFile = "Metrics.txt", >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?illuminaAnnotation="Humanv4") >> Processing section 5168671015_A_1 >> Processing section 5168671015_B_1 >> Processing section 5168671015_C_1 >> Processing section 5168671015_D_1 >> Processing section 5168671015_E_1 >> Processing section 5168671015_F_1 >> Processing section 5168671015_G_1 >> Processing section 5168671015_H_1 >> Processing section 5168671015_I_1 >> Processing section 5168671015_J_1 >> Processing section 5168671015_K_1 >> Processing section 5168671015_L_1 >>> ? ? dir2 ? ? <- "/5168671022" >>> ? ? iBatch2 ?<- readIllumina(dir = paste(".", dir2, sep = ""), >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?useImages = FALSE, >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?metricsFile = "Metrics.txt", >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?illuminaAnnotation="Humanv4") >> Processing section 5168671022_A_1 >> Processing section 5168671022_B_1 >> Processing section 5168671022_C_1 >> Processing section 5168671022_D_1 >> Processing section 5168671022_E_1 >> Processing section 5168671022_F_1 >> Processing section 5168671022_G_1 >> Processing section 5168671022_H_1 >> Processing section 5168671022_I_1 >> Processing section 5168671022_J_1 >> Processing section 5168671022_K_1 >> Processing section 5168671022_L_1 >>> iBatch = combine(iBatch1,iBatch2) >> Error in combine(iBatch1, iBatch2) : unable to combine these objects >>> class(iBatch1) >> [1] "beadLevelData" >> attr(,"package") >> [1] "beadarray" >>> class(iBatch2) >> [1] "beadLevelData" >> attr(,"package") >> [1] "beadarray" >> >> On Tue, 7 Dec 2010 10:46:21 +0000, Mark Dunning <mark.dunning at="" gmail.com=""> >> wrote: >>> Hi Alex, >>> >>> The functionality still exists in beadarray, but can be called using >>> the generic 'combine' rather than combineBeadLevelLists. >>> >>> Best wishes, >>> >>> Mark >>> >>> On Tue, Dec 7, 2010 at 10:20 AM, Alex Gutteridge >>> <alexg at="" ruggedtextile.com=""> wrote: >>>> Hi, >>>> >>>> Older versions of beadarray have a combineBeadLevelList() for combining >>>> bead level data lists read from two different Illumina chips into one >>>> list. >>>> In the latest beadarray this seems to have been removed, but I can't >> find >>>> anything in the documentation describing the correct way to do this >> with >>>> the new beadLevelData class. Am I missing something obvious or is this >> no >>>> longer supported? >>>> >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> Platform: x86_64-unknown-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] splines ? stats ? ? graphics ?grDevices utils ? ? datasets >>>> ?methods >>>> [8] base >>>> >>>> other attached packages: >>>> ?[1] reshape_0.8.3 ? ? ? ? ?plyr_1.2.1 ? ? ? ? ? ? nlme_3.1-97 >>>> ?[4] lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 ? ? RSQLite_0.9-3 >>>> ?[7] DBI_0.2-5 ? ? ? ? ? ? ?AnnotationDbi_1.12.0 ? lumi_2.2.0 >>>> [10] limma_3.6.6 ? ? ? ? ? ?latticeExtra_0.6-14 ? ?RColorBrewer_1.0-2 >>>> [13] lattice_0.19-13 ? ? ? ?contrast_0.13 ? ? ? ? ?Design_2.3-0 >>>> [16] Hmisc_3.8-3 ? ? ? ? ? ?survival_2.36-1 ? ? ? ?Cairo_1.4-5 >>>> [19] beadarray_2.0.2 ? ? ? ?Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> ?[1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.0 >>>> ?[4] cluster_1.13.2 ? ? ? ?grid_2.12.0 ? ? ? ? ? hdrcde_2.14 >>>> ?[7] KernSmooth_2.23-4 ? ? MASS_7.3-8 ? ? ? ? ? ?Matrix_0.999375-44 >>>> [10] methylumi_1.4.0 ? ? ? mgcv_1.7-1 ? ? ? ? ? ?preprocessCore_1.12.0 >>>> [13] tcltk_2.12.0 ? ? ? ? ?tools_2.12.0 ? ? ? ? ?xtable_1.5-6 >>>> >>>> -- >>>> Alex Gutteridge >>>> >>>> _______________________________________________ >>>> 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 >>>> >> >> -- >> Alex Gutteridge >> -- Alex Gutteridge
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