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Question: lumiR returns ExpressionSet object instead of LumiBatch
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5.4 years ago by
Guest User12k
Guest User12k wrote:
Hello, It is my first time trying to use lumi package to analyze beadchip data by following the instruction in vignettes (dated 2013/4/4). However I run into problems. Trying to use lumiR to read in a beadstudio export file with following commands: library(lumi) library(illumi sampfile <- 'path/to/sample_probe_profile.txt' lumi.sample<-lumiR(sampfile, lib.mapping="lumiMouseIDMapping", annotationColumn = c('PROBE_ID', 'SYMBOL', 'ILMN_GENE', 'CHROMOSOME', 'DEFINITION', 'SYNONYMS') ) It runs without error, but class(lumi.sample) tells me that it is an ExpressionSet object not LumiBatch. And of course I cannt apply lumi methods to analyze it. What wrong with my steps? Thanks! Here is the first 15 lines of the probe_profile file: PROBE_ID SYMBOL NT1.AVG_Signal NT1.Detection Pval NT2.AVG_Signal NT2.Detection Pval NT3.AVG_Signal NT3.Detection Pval R1.AVG_Signal R1.Detection PvalR2.AVG_Signal R2.Detection Pval R3.AVG_Signal R3.Detection Pval M1_2.AVG_Signal M1_2.Detection Pval HG1_2.AVG_Signal HG1_2.Detection Pval M1.AVG_Signal M1.Detection Pval M2.AVG_Signal M2.Detection Pval M3.AVG_Signal M3.Detection Pval HG1.AVG_Signal HG1.Detection Pval HG2.AVG_Signal HG2.Detection Pval HG3.AVG_Signal HG3.Detection Pval NT1_2.AVG_Signal NT1_2.Detection Pval R1_2.AVG_Signal R1_2.Detection Pval SEARCH_KEY ILMN_GENE CHROMOSOME DEFINITION SYNONYMS ILMN_2896528 0610006I08Rik 2607.672 0.00 2527.176 0.00 2774.688 0.00 1997.495 0.00 2124.155 0.00 2544.899 0.00 3062.838 0.00 3381.947 0.00 2546.513 0.00 3017.973 0.00 2987.024 0.00 3376.653 0.00 2492.156 0.00 3577.373 0.00 2659.114 0.00 2353.836 0.00 ILMN_220369 0610006I08RIK 19 Mus musculus RIKEN cDNA 0610006I08 gene (0610006I08Rik), mRNA. ILMN_2721178 0610006I08Rik 335.6214 0.00 309.3783 0.00 311.5328 0.00 255.2664 0.00 253.7414 0.00 304.8765 0.00 363.3045 0.00 416.1963 0.00 285.1985 0.00 417.5847 0.00 356.8044 0.00 371.7544 0.00 308.4683 0.00 533.7448 0.00 304.7859 0.00 259.3861 0.00 ILMN_220369 0610006I08RIK 19 Mus musculus RIKEN cDNA 0610006I08 gene (0610006I08Rik), mRNA. ILMN_3033922 0610007C21Rik 1435.676 0.00 1407.494 0.00 1813.653 0.00 1138.474 0.00 1199.863 0.00 1369.412 0.00 1186.747 0.00 1436.43 0.00 1138.299 0.00 1344.861 0.00 1320.021 0.00 1378.295 0.00 1026.762 0.00 1909.174 0.00 1361.688 0.00 1232.837 0.00 ILMN_244468 0610007C21RIK 5 Mus musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 1, mRNA. AI316792; HSPC013; Apr3; p18 ILMN_3092673 0610007C21Rik 11323.47 0.00 9251.417 0.00 11511.11 0.00 9007.652 0.00 8195.785 0.00 9388.674 0.00 9282.038 0.00 9625.286 0.00 8375.805 0.00 9982.474 0.00 9821.961 0.00 9076.46 0.00 7963.4 0.00 9219.595 0.00 10254.2 0.00 9168.383 0.00 ILMN_229637 0610007C21RIK 5 Mus musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 2, mRNA. AI316792; HSPC013; Apr3; p18 ILMN_2816356 0610007P08Rik 25.62827 0.09398496 45.53978 0.02380952 0.5504513 0.3784461 23.20286 0.0989975 7.337133 0.2568922 16.80947 0.1566416 18.40724 0.1478697 31.25397 0.0764411 0.1861096 0.3759398 10.07403 0.2255639 16.067 0.1503759 21.37516 0.1027569 6.433805 0.2393484 24.07508 0.08646616 24.31498 0.08646616 26.45578 0.08270676 ILMN_196322 0610007P08RIK 13 Mus musculus RIKEN cDNA 0610007P08 gene (0610007P08Rik), transcript variant 2, mRNA. RAD26L; 1700019D06Rik ILMN_2808939 0610007P14Rik 712.1257 0.00 624.3039 0.00 779.4008 0.00 695.1705 0.00 671.4506 0.00 787.93 0.00 756.97860.00 476.1805 0.00 574.3113 0.00 746.5471 0.00 743.4769 0.00 422.7865 0.00 376.804 0.00 620.1172 0.00 607.81810.00 753.4628 0.00 ILMN_239772 0610007P14RIK 12 Mus musculus RIKEN cDNA 0610007P14 gene (0610007P14Rik), mRNA. AU019315; C77855; 1190004E09Rik; ORF11 ILMN_2634564 0610007P22Rik 595.3325 0.00 451.3885 0.00 580.5104 0.00 371.2965 0.00 492.7807 0.00 479.4933 0.00 549.2484 0.00 494.6838 0.00 401.5907 0.00 437.3422 0.00 539.7564 0.00 471.3762 0.00 331.5264 0.00 516.2159 0.00 535.5032 0.00 477.19 0.00 ILMN_213192 0610007P22RIK 17 Mus musculus RIKEN cDNA 0610007P22 gene (0610007P22Rik), mRNA. AL022759; MGC113771; 1110014B11Rik ILMN_2737647 0610008C08Rik -0.5213413 0.4085213 7.743881 0.254386 4.068563 0.3157895 6.312949 0.2593985 7.170675 0.2606516 10.64135 0.2155388 25.66834 0.0877193 7.385303 0.2593985 -5.414614 0.5413534 0.8812458 0.3822055 14.31114 0.1716792 -3.741079 0.5012531 13.13283 0.1390978 -2.912084 0.4724311 -13.54885 0.8233083 -6.836047 0.6052632ILMN_221600 0610008C08RIK X Mus musculus RIKEN cDNA 0610008C08 gene (0610008C08Rik), mRNA. RP23-272D10.2; MGC130105; MGC130106; 1110019O03Rik ILMN_2734484 0610009B22Rik 1660.084 0.00 1600.733 0.00 1853.014 0.00 1533.854 0.00 1641.063 0.00 1688.237 0.00 1758.677 0.00 1718.719 0.00 1528.311 0.00 1867.37 0.00 1768.41 0.00 1607.629 0.00 1211.871 0.00 1692.573 0.00 1825.8470.00 1744.845 0.00 ILMN_221361 0610009B22RIK 11 Mus musculus RIKEN cDNA 0610009B22 gene (0610009B22Rik), mRNA. RP23-79E13.7 ILMN_2952292 0610009D07Rik 161.6432 0.00 150.4215 0.00 216.1236 0.00 169.6933 0.00 141.3559 0.00 208.3837 0.00 183.1769 0.00 113.102 0.00 145.3057 0.00 174.5983 0.00 196.8766 0.00 98.69936 0.00 85.1308 0.00 135.3256 0.00 207.43860.00 199.6864 0.00 ILMN_218698 0610009D07RIK 12 Mus musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA. 6030419K15Rik; AV001342; Sf3b14 ILMN_2699078 0610009D07Rik -13.64666 0.7719298 -17.76805 0.9285714 -13.25819 0.7243108 -7.510522 0.6127819 -21.9306 0.9699248 -17.45373 0.8696742 -19.45185 0.9360902 -9.678173 0.6303258 -5.608812 0.5501253 -10.17932 0.6729323 -17.24747 0.8746867 -16.90044 0.9172933 -8.415766 0.7230576 -11.58076 0.7481203 -20.62218 0.9761904 -9.215716 0.6654136 ILMN_218698 0610009D07RIK 12 Mus musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA. 6030419K15Rik; AV001342; Sf3b14 ILMN_1213681 0610009O20Rik 177.286 0.00 146.7101 0.00 148.6533 0.00 136.2325 0.00 194.6553 0.00 193.7644 0.00 165.37730.00 167.7943 0.00 163.8992 0.00 221.8292 0.00 197.5723 0.00 203.4886 0.00 139.8207 0.00 300.4458 0.00 163.7285 0.00 179.5151 0.00 ILMN_220613 0610009O20RIK 18 Mus musculus RIKEN cDNA 0610009O20 gene (0610009O20Rik), mRNA. 2700004E22Rik ILMN_2735413 0610010D20Rik 7.146307 0.2706767 7.9561 0.2468672 24.70525 0.1102757 5.685019 0.2719298 10.20794 0.2155388-4.846704 0.5213032 -3.845815 0.4874687 -6.052074 0.5238096 -6.612185 0.5827067 1.393941 0.3759398 -11.49365 0.735589 1.478938 0.3558897 5.659925 0.2506266 9.050623 0.226817 -2.104225 0.4398496 -15.24391 0.8558897 ILMN_221425 0610010D20RIK 19 Mus musculus RIKEN cDNA 0610010D20 gene (0610010D20Rik), mRNA. ILMN_2735415 0610010D20Rik -11.26077 0.7067669 -0.4047703 0.4035088 6.900579 0.2807018 0.7097692 0.3834586 -7.749537 0.6215539 -16.24752 0.8446115 17.96398 0.1503759 5.702412 0.2819549 5.526793 0.2869674 11.87896 0.2017544 1.067933 0.3734336 -10.01922 0.7205514 -0.05420115 0.4110276 -3.374624 0.4837093 12.72869 0.1691729 -8.716571 0.6453634ILMN_221425 0610010D20RIK 19 Mus musculus RIKEN cDNA 0610010D20 gene (0610010D20Rik), mRNA. -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.12.2 [3] lumiMouseIDMapping_1.10.0 lumi_2.12.0 [5] BSgenome.Scerevisiae.UCSC.sacCer1_1.3.17 sagenhaft_1.30.0 [7] SparseM_0.99 edgeR_3.2.3 [9] limma_3.16.5 hexbin_1.26.2 [11] BSgenome_1.28.0 ShortRead_1.18.0 [13] latticeExtra_0.6-24 RColorBrewer_1.0-5 [15] lattice_0.20-15 Rsamtools_1.12.3 [17] Biostrings_2.28.0 rtracklayer_1.20.2 [19] GenomicRanges_1.12.4 IRanges_1.18.1 [21] gaschYHS_1.0.11 org.Hs.eg.db_2.9.0 [23] org.Sc.sgd.db_2.9.1 BiocInstaller_1.10.2 [25] GO.db_2.9.0 RSQLite_0.11.4 [27] DBI_0.2-7 AnnotationDbi_1.22.6 [29] Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 beanplot_1.1 [5] biomaRt_2.16.0 bitops_1.0-5 colorspace_1.2-2 hwriter_1.3 [9] illuminaio_0.2.0 KernSmooth_2.23-10 MASS_7.3-26 Matrix_1.0-12 [13] matrixStats_0.8.1 mclust_4.1 methylumi_2.6.1 mgcv_1.7-24 [17] minfi_1.6.0 multtest_2.16.0 nleqslv_2.0 nlme_3.1-109 [21] nor1mix_1.1-4 preprocessCore_1.22.0 R.methodsS3_1.4.2 RCurl_1.95-4.1 [25] reshape_0.8.4 siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 [29] survival_2.37-4 tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 [33] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.4 years ago by Pan Du440 • written 5.4 years ago by Guest User12k
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5.4 years ago by
Pan Du440
Pan Du440 wrote:
Hi Liu X This is because your data does not include the bead standard error information for the probes (columns are named like "BEAD_STDERR"), which is required for LumiBatch class. If this information is missing, the lumiR will just output an ExpressionSet object. Please check the help of lumiR and the lumi.pdf vignette for more details. Pan On Thu, Jun 27, 2013 at 7:30 PM, Liu X [guest] <guest@bioconductor.org>wrote: > > Hello, > > It is my first time trying to use lumi package to analyze beadchip data by > following the instruction in vignettes (dated 2013/4/4). However I run into > problems. Trying to use lumiR to read in a beadstudio export file with > following commands: > > library(lumi) > library(illumi > sampfile <- 'path/to/sample_probe_profile.txt' > lumi.sample<-lumiR(sampfile, lib.mapping="lumiMouseIDMapping", > annotationColumn = c('PROBE_ID', 'SYMBOL', 'ILMN_GENE', 'CHROMOSOME', > 'DEFINITION', 'SYNONYMS') ) > > It runs without error, but class(lumi.sample) tells me that it is an > ExpressionSet object not LumiBatch. And of course I cannt apply lumi > methods to analyze it. > > What wrong with my steps? > > Thanks! > > Here is the first 15 lines of the probe_profile file: > PROBE_ID SYMBOL NT1.AVG_Signal NT1.Detection Pval > NT2.AVG_Signal NT2.Detection Pval NT3.AVG_Signal NT3.Detection Pval > R1.AVG_Signal R1.Detection PvalR2.AVG_Signal R2.Detection Pval > R3.AVG_Signal R3.Detection Pval M1_2.AVG_Signal M1_2.Detection > Pval HG1_2.AVG_Signal HG1_2.Detection Pval M1.AVG_Signal > M1.Detection Pval M2.AVG_Signal M2.Detection Pval > M3.AVG_Signal M3.Detection Pval HG1.AVG_Signal HG1.Detection Pval > HG2.AVG_Signal HG2.Detection Pval HG3.AVG_Signal HG3.Detection > Pval NT1_2.AVG_Signal NT1_2.Detection Pval R1_2.AVG_Signal > R1_2.Detection Pval SEARCH_KEY ILMN_GENE CHROMOSOME > DEFINITION SYNONYMS > ILMN_2896528 0610006I08Rik 2607.672 0.00 2527.176 > 0.00 2774.688 0.00 1997.495 0.00 2124.155 > 0.00 2544.899 0.00 3062.838 0.00 3381.947 0.00 > 2546.513 0.00 3017.973 0.00 2987.024 0.00 > 3376.653 0.00 2492.156 0.00 3577.373 0.00 > 2659.114 0.00 2353.836 0.00 ILMN_220369 > 0610006I08RIK 19 Mus musculus RIKEN cDNA 0610006I08 gene > (0610006I08Rik), mRNA. > ILMN_2721178 0610006I08Rik 335.6214 0.00 309.3783 > 0.00 311.5328 0.00 255.2664 0.00 253.7414 > 0.00 304.8765 0.00 363.3045 0.00 416.1963 0.00 > 285.1985 0.00 417.5847 0.00 356.8044 0.00 > 371.7544 0.00 308.4683 0.00 533.7448 0.00 > 304.7859 0.00 259.3861 0.00 ILMN_220369 > 0610006I08RIK 19 Mus musculus RIKEN cDNA 0610006I08 gene > (0610006I08Rik), mRNA. > ILMN_3033922 0610007C21Rik 1435.676 0.00 1407.494 > 0.00 1813.653 0.00 1138.474 0.00 1199.863 > 0.00 1369.412 0.00 1186.747 0.00 1436.43 0.00 1138.299 > 0.00 1344.861 0.00 1320.021 0.00 1378.295 > 0.00 1026.762 0.00 1909.174 0.00 1361.688 0.00 > 1232.837 0.00 ILMN_244468 0610007C21RIK 5 Mus > musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 1, > mRNA. AI316792; HSPC013; Apr3; p18 > ILMN_3092673 0610007C21Rik 11323.47 0.00 9251.417 > 0.00 11511.11 0.00 9007.652 0.00 8195.785 > 0.00 9388.674 0.00 9282.038 0.00 9625.286 0.00 > 8375.805 0.00 9982.474 0.00 9821.961 0.00 > 9076.46 0.00 7963.4 0.00 9219.595 0.00 10254.2 0.00 > 9168.383 0.00 ILMN_229637 0610007C21RIK 5 Mus > musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 2, > mRNA. AI316792; HSPC013; Apr3; p18 > ILMN_2816356 0610007P08Rik 25.62827 0.09398496 45.53978 > 0.02380952 0.5504513 0.3784461 23.20286 > 0.0989975 7.337133 0.2568922 16.80947 0.1566416 > 18.40724 0.1478697 31.25397 0.0764411 > 0.1861096 0.3759398 10.07403 0.2255639 16.067 > 0.1503759 21.37516 0.1027569 6.433805 0.2393484 > 24.07508 0.08646616 24.31498 0.08646616 > 26.45578 0.08270676 ILMN_196322 0610007P08RIK 13 > Mus musculus RIKEN cDNA 0610007P08 gene (0610007P08Rik), transcript > variant 2, mRNA. RAD26L; 1700019D06Rik > ILMN_2808939 0610007P14Rik 712.1257 0.00 624.3039 > 0.00 779.4008 0.00 695.1705 0.00 671.4506 > 0.00 787.93 0.00 756.97860.00 476.1805 0.00 574.3113 > 0.00 746.5471 0.00 743.4769 0.00 422.7865 > 0.00 376.804 0.00 620.1172 0.00 607.81810.00 > 753.4628 0.00 ILMN_239772 0610007P14RIK 12 Mus > musculus RIKEN cDNA 0610007P14 gene (0610007P14Rik), mRNA. AU019315; > C77855; 1190004E09Rik; ORF11 > ILMN_2634564 0610007P22Rik 595.3325 0.00 451.3885 > 0.00 580.5104 0.00 371.2965 0.00 492.7807 > 0.00 479.4933 0.00 549.2484 0.00 494.6838 0.00 > 401.5907 0.00 437.3422 0.00 539.7564 0.00 > 471.3762 0.00 331.5264 0.00 516.2159 0.00 > 535.5032 0.00 477.19 0.00 ILMN_213192 0610007P22RIK 17 > Mus musculus RIKEN cDNA 0610007P22 gene (0610007P22Rik), mRNA. > AL022759; MGC113771; 1110014B11Rik > ILMN_2737647 0610008C08Rik -0.5213413 0.4085213 7.743881 > 0.254386 4.068563 0.3157895 6.312949 > 0.2593985 7.170675 0.2606516 10.64135 0.2155388 > 25.66834 0.0877193 7.385303 0.2593985 > -5.414614 0.5413534 0.8812458 0.3822055 14.31114 > 0.1716792 -3.741079 0.5012531 13.13283 0.1390978 > -2.912084 0.4724311 -13.54885 0.8233083 > -6.836047 0.6052632ILMN_221600 0610008C08RIK X Mus > musculus RIKEN cDNA 0610008C08 gene (0610008C08Rik), mRNA. RP23-272D10.2; > MGC130105; MGC130106; 1110019O03Rik > ILMN_2734484 0610009B22Rik 1660.084 0.00 1600.733 > 0.00 1853.014 0.00 1533.854 0.00 1641.063 > 0.00 1688.237 0.00 1758.677 0.00 1718.719 0.00 > 1528.311 0.00 1867.37 0.00 1768.41 0.00 1607.629 > 0.00 1211.871 0.00 1692.573 0.00 1825.8470.00 > 1744.845 0.00 ILMN_221361 0610009B22RIK 11 Mus > musculus RIKEN cDNA 0610009B22 gene (0610009B22Rik), mRNA. RP23-79E13.7 > ILMN_2952292 0610009D07Rik 161.6432 0.00 150.4215 > 0.00 216.1236 0.00 169.6933 0.00 141.3559 > 0.00 208.3837 0.00 183.1769 0.00 113.102 0.00 145.3057 > 0.00 174.5983 0.00 196.8766 0.00 98.69936 > 0.00 85.1308 0.00 135.3256 0.00 207.43860.00 > 199.6864 0.00 ILMN_218698 0610009D07RIK 12 Mus > musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA. 6030419K15Rik; > AV001342; Sf3b14 > ILMN_2699078 0610009D07Rik -13.64666 0.7719298 -17.76805 > 0.9285714 -13.25819 0.7243108 -7.510522 > 0.6127819 -21.9306 0.9699248 -17.45373 0.8696742 > -19.45185 0.9360902 -9.678173 0.6303258 > -5.608812 0.5501253 -10.17932 0.6729323 -17.24747 > 0.8746867 -16.90044 0.9172933 -8.415766 > 0.7230576 -11.58076 0.7481203 -20.62218 0.9761904 > -9.215716 0.6654136 ILMN_218698 0610009D07RIK 12 > Mus musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA. > 6030419K15Rik; AV001342; Sf3b14 > ILMN_1213681 0610009O20Rik 177.286 0.00 146.7101 0.00 > 148.6533 0.00 136.2325 0.00 194.6553 0.00 > 193.7644 0.00 165.37730.00 167.7943 0.00 163.8992 > 0.00 221.8292 0.00 197.5723 0.00 203.4886 > 0.00 139.8207 0.00 300.4458 0.00 163.7285 0.00 > 179.5151 0.00 ILMN_220613 0610009O20RIK 18 Mus > musculus RIKEN cDNA 0610009O20 gene (0610009O20Rik), mRNA. 2700004E22Rik > ILMN_2735413 0610010D20Rik 7.146307 0.2706767 7.9561 > 0.2468672 24.70525 0.1102757 5.685019 0.2719298 > 10.20794 0.2155388-4.846704 0.5213032 -3.845815 > 0.4874687 -6.052074 0.5238096 -6.612185 > 0.5827067 1.393941 0.3759398 -11.49365 0.735589 > 1.478938 0.3558897 5.659925 0.2506266 9.050623 > 0.226817 -2.104225 0.4398496 -15.24391 > 0.8558897 ILMN_221425 0610010D20RIK 19 Mus musculus RIKEN > cDNA 0610010D20 gene (0610010D20Rik), mRNA. > ILMN_2735415 0610010D20Rik -11.26077 0.7067669 -0.4047703 > 0.4035088 6.900579 0.2807018 0.7097692 > 0.3834586 -7.749537 0.6215539 -16.24752 0.8446115 > 17.96398 0.1503759 5.702412 0.2819549 > 5.526793 0.2869674 11.87896 0.2017544 1.067933 > 0.3734336 -10.01922 0.7205514 -0.05420115 0.4110276 > -3.374624 0.4837093 12.72869 0.1691729 > -8.716571 0.6453634ILMN_221425 0610010D20RIK 19 Mus > musculus RIKEN cDNA 0610010D20 gene (0610010D20Rik), mRNA. > > > > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.12.2 > [3] lumiMouseIDMapping_1.10.0 lumi_2.12.0 > [5] BSgenome.Scerevisiae.UCSC.sacCer1_1.3.17 sagenhaft_1.30.0 > [7] SparseM_0.99 edgeR_3.2.3 > [9] limma_3.16.5 hexbin_1.26.2 > [11] BSgenome_1.28.0 ShortRead_1.18.0 > [13] latticeExtra_0.6-24 RColorBrewer_1.0-5 > [15] lattice_0.20-15 Rsamtools_1.12.3 > [17] Biostrings_2.28.0 rtracklayer_1.20.2 > [19] GenomicRanges_1.12.4 IRanges_1.18.1 > [21] gaschYHS_1.0.11 org.Hs.eg.db_2.9.0 > [23] org.Sc.sgd.db_2.9.1 BiocInstaller_1.10.2 > [25] GO.db_2.9.0 RSQLite_0.11.4 > [27] DBI_0.2-7 AnnotationDbi_1.22.6 > [29] Biobase_2.20.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 > beanplot_1.1 > [5] biomaRt_2.16.0 bitops_1.0-5 colorspace_1.2-2 > hwriter_1.3 > [9] illuminaio_0.2.0 KernSmooth_2.23-10 MASS_7.3-26 > Matrix_1.0-12 > [13] matrixStats_0.8.1 mclust_4.1 methylumi_2.6.1 > mgcv_1.7-24 > [17] minfi_1.6.0 multtest_2.16.0 nleqslv_2.0 > nlme_3.1-109 > [21] nor1mix_1.1-4 preprocessCore_1.22.0 R.methodsS3_1.4.2 > RCurl_1.95-4.1 > [25] reshape_0.8.4 siggenes_1.34.0 splines_3.0.1 > stats4_3.0.1 > [29] survival_2.37-4 tools_3.0.1 XML_3.95-0.2 > xtable_1.7-1 > [33] zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.4 years ago by Pan Du440
Hi Pan, Thank you very much for pointing it out. I asked the lab to include the columns and export again. Worked perfectly. I almost finished analysis now. Thanks! Xiao-yu On 6/28/13 1:38 AM, Pan Du wrote: > Hi Liu X > > This is because your data does not include the bead standard error > information for the probes (columns are named like "BEAD_STDERR"), > which is required for LumiBatch class. If this information is missing, > the lumiR will just output an ExpressionSet object. Please check the > help of lumiR and the lumi.pdf vignette for more details. > > > Pan > > > On Thu, Jun 27, 2013 at 7:30 PM, Liu X [guest] <guest@bioconductor.org> <mailto:guest@bioconductor.org>> wrote: > > > Hello, > > It is my first time trying to use lumi package to analyze beadchip > data by following the instruction in vignettes (dated 2013/4/4). > However I run into problems. Trying to use lumiR to read in a > beadstudio export file with following commands: > > library(lumi) > library(illumi > sampfile <- 'path/to/sample_probe_profile.txt' > lumi.sample<-lumiR(sampfile, lib.mapping="lumiMouseIDMapping", > annotationColumn = c('PROBE_ID', 'SYMBOL', 'ILMN_GENE', > 'CHROMOSOME', 'DEFINITION', 'SYNONYMS') ) > > It runs without error, but class(lumi.sample) tells me that it is > an ExpressionSet object not LumiBatch. And of course I cannt apply > lumi methods to analyze it. > > What wrong with my steps? > > Thanks! > [[alternative HTML version deleted]]
ADD REPLYlink written 5.4 years ago by Xiao-yu Liu10
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