lumiR error
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@paul-sanfilippo-3894
Last seen 9.6 years ago
Dear List, I'm new to microarray analysis, so go easy. When I try to import some methylation data using lumiR, I receive the following error: > meth<-lumiR("~/desktop/meth_sample.txt") Error in gregexpr("\t", dataLine1) : invalid 'text' argument If I specify "sep": > meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : subscript out of bounds Does anyone know what might be causing the problem? Can lumiR handle this type of data where headers from BeadStudio are "..._Beta" instead of "..._Signal", etc Thank you, Paul Sanfilippo
Microarray GO Microarray GO • 2.5k views
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Pan Du ★ 1.2k
@pan-du-2010
Last seen 9.6 years ago
Hi Paul Please provide more detailed information, or else we cannot help you. For example, please send me the returns of sessionInfo() and also the top twenty lines of your data. I want to know whether it is because you are using outdated packages or data in the wrong format. Thanks! Pan On 1/16/10 5:24 PM, "gilbert feng" <g-feng at="" northwestern.edu=""> wrote: > From: Paul Sanfilippo <prseye at="" gmail.com=""> > Date: Sun, 17 Jan 2010 10:16:41 +1100 > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] lumiR error > > Dear List, > > I'm new to microarray analysis, so go easy. When I try to import some > methylation data using lumiR, I receive the following error: > >> meth<-lumiR("~/desktop/meth_sample.txt") > Error in gregexpr("\t", dataLine1) : invalid 'text' argument > > If I specify "sep": > >> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") > Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : > subscript out of bounds > > Does anyone know what might be causing the problem? Can lumiR handle > this type of data where headers from BeadStudio are "..._Beta" instead > of "..._Signal", etc > > Thank you, > > Paul Sanfilippo -- Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan (at) northwestern.edu
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Hi Pan, I'm thinking the data is in the wrong format, but am keen to know if there's a way around this (eg remapping column headers) > sessionInfo() R version 2.10.1 Patched (2009-12-29 r50852) x86_64-apple-darwin9.8.0 locale: [1] C/C/en_US/C/C/C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1 [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 [7] affy_1.24.2 annotate_1.24.1 AnnotationDbi_1.8.1 [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2 [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8 [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2 [19] rJava_0.8-1 loaded via a namespace (and not attached): [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26 nlme_3.1-96 [5] tools_2.10.1 xtable_1.5-6 > This is the data format that I have (I've just included the first subject columns (in yellow)) Index TargetID ProbeID_A ProbeID_B 4408100018_A.AVG_Beta 4408100018_A.Intensity 4408100018_A.Avg_NBEADS_A 4408100018_A.Avg_NBEADS_B 4408100018_A.BEAD_STDERR_A 4408100018_A.BEAD_STDERR_B 4408100018_A.Signal_A 4408100018_A.Signal_B 4408100018_A.Detection Pval SYMBOL ILMNID NAME ILMNSTRAND ADDRESSA_ID ALLELEA_PROBESEQ ADDRESSB_ID ALLELEB_PROBESEQ GENOMEBUILD CHR MAPINFO PLOIDY SPECIES SOURCE SOURCEVERSION SOURCESTRAND SOURCESEQ TOPGENOMICSEQ NEXT_BASE COLOR_CHANNEL TSS_COORDINATE GENE_STRAND GENE_ID SYNONYM ACCESSION GID ANNOTATION PRODUCT DISTANCE_TO_TSS CPG_ISLAND CPG_ISLAND_LOCATIONS 1 cg00000292 990370 6660678 0.7628557 1903 17 26 33.71245 83.91733 375 1528 1.83E-24 ATP2A1 cg00000292 cg00000292 TOP 990370 AAACATTAATTACCAACCACTCTTCCAAAAAACACTTACCATTAAAACCA 6660678 AAACATTAATTACCAACCGCTCTTCCAAAAAACACTTACCATTAAAACCG 36 16 28797601 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGGCCTCAATGGTAAGTGTCCCTTGGAAGAGCGGCTGGTAATTAATGCCC TGGGGTGAGTGAGACCACGGGCCTCACCCCGGACCAAGTTAAGCGGAATCTGGAGAAATA[CG]GCCTCA ATGGTAAGTGTCCCTTGGAAGAGCGGCTGGTAATTAATGCCCTCCTGCACCCCC T Red 28797310 + GeneID:487 ATP2A; SERCA1; NM_173201.2 GI:47132613 isoform a is encoded by transcript variant a; sarcoplasmic/endoplasmic reticulum calcium ATPase 1; calcium pump 1; SR Ca(2+)-ATPase 1; calcium-transporting ATPase sarcoplasmic reticulum type; fast twitch skeletal muscle isoform; endoplasmic reticulum class 1/2 Ca(2+) ATPase; go_component: membrane; go_component: integral to membrane; go_component: sarcoplasmic reticulum; go_component: smooth endoplasmic reticulum; go_function: ATP binding; go_function: hydrolase activity; go_function: nucleotide binding; go_function: calcium ion binding; go_function: magnesium ion binding; go_function: calcium-transporting ATPase activity; go_function: hydrolase activity; acting on acid anhydrides; catalyzing transmembrane movement of substances; go_process: metabolism; go_process: cation transport; go_process: proton transport; go_process: calcium ion transport; go_process: regulation of striated muscle contraction ATPase; Ca++ transporting; fast twitch 1 isoform a 291 TRUE 16:28797486-28797825 2 cg00002426 6580397 6100343 0.7422037 1343 17 28 14.06707 82.46211 272 1071 2.98E-09 SLMAP cg00002426 cg00002426 TOP 6580397 AATATAATAACATTACCTTACCCATCTTATAATCAAACCAAACAAAAACA 6100343 AATATAATAACATTACCTTACCCGTCTTATAATCAAACCAAACGAAAACG 36 3 57718583 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGCTCTCGTCTGGTTTGATCACAAGACGGGCAAGGTAATGTCACCACATT CCGCTGTCGACCAGCGCAGAATAATGCCACTTTTGATTGCAAAGTGCTATCAAGGAACCA[CG]CTCTCG TCTGGTTTGATCACAAGACGGGCAAGGTAATGTCACCACATTGTCCAGCGGCAT T Red 57718214 + GeneID:7871 SLAP; KIAA1601; NM_007159.2 GI:56550042 Sarcolemmal-associated protein; go_component: integral to plasma membrane; go_component: smooth endoplasmic reticulum; go_function: unfolded protein binding; go_process: protein folding; go_process: muscle contraction sarcolemma associated protein 369 TRUE 3:57716811-57718675 3 cg00003994 7150184 7150392 0.06791084 1829 17 9 124.9058 8.246211 1698 131 5.38E-22 MEOX2 cg00003994 cg00003994 TOP 7150184 AATAATAATAATACCCCCTATAATACTAACTAACAAACATACCCTCTTCA 7150392 AATAATAATAATACCCCCTATAATACTAACTAACAAACATACCCTCTTCG 36 7 15692387 diploid Homo sapiens NCBI:RefSeq 36.1 BOT GGTGGTGGTGGTGCCCCCTGTGATGCTGGCTGGCAAACATGCCCTCTTCG GGTGGTGGTGGTGGTGGTGGTGGTGCCCCCTGTGATGCTGGCTGGCAAACATGCCCTCTT[CG]TTGGGG TATCCCGCGATTATGCAAGATGAGGAAGAAGTAGAGAGCTCGGGGTAAGACATA T Red 15692819 - GeneID:4223 GAX; MOX2; NM_005924.3 GI:55956906 growth arrest-specific homeo box; go_component: nucleus; go_function: transcription factor activity; go_process: circulation; go_process: development; go_process: regulation of transcription; DNA-dependent mesenchyme homeo box 2 432 TRUE 7:15691512-15693551 4 cg00005847 4850717 1260113 0.1226525 7621 15 15 726.3135 101.7304 6674 947 3.68E-38 HOXD3 cg00005847 cg00005847 BOT 4850717 TACTATAATACACCCTATATTTAAAACACTAAACTTACCCCATTAAAACA 1260113 TACTATAATACACCCTATATTTAAAACACTAAACTTACCCCATTAAAACG 36 2 176737319 diploid Homo sapiens NCBI:RefSeq 36.1 BOT TACTGTAATGCACCCTGTATTTAAGGCACTGGGCTTGCCCCATTAAAGCG CAGATAACTCAATACTGTAATGCACCCTGTATTTAAGGCACTGGGCTTGCCCCATTAAAG[CG]CCATAA ATTTGAAGGCCAATGATCGGTTTTCATGTAACGGGTGGTACTTCATACTGAAGT C Grn 176737051 + GeneID:3232 HOX4; HOX1D; HOX4A; Hox-4.1; MGC10470; NM_006898.4 GI:23510372 homeobox protein Hox-D3; Hox-4.1; mouse; homolog of; homeo box D3; go_component: nucleus; go_function: transcription factor activity; go_process: morphogenesis; go_process: regulation of transcription; DNA-dependent homeobox D3 268 FALSE 5 cg00006414 6980731 4280093 0.07699007 5641 26 19 321.6305 23.73005 5199 442 3.68E-38 ZNF398 cg00006414 cg00006414 BOT 6980731 CTCAAAAACCAAACAAAACAAAACCCCAATACTAATCATTAATAAAATCA 4280093 CTCGAAAACCGAACAAAACAAAACCCCAATACTAATCGTTAATAAAATCG 36 7 148453770 diploid Homo sapiens NCBI:RefSeq 36.1 BOT CTCGGAAACCGAGCAGGGCAAAACCCCAGTGCTGATCGTTAGTGGGATCG GAACCGGCCCAGCTCGGAAACCGAGCAGGGCAAAACCCCAGTGCTGATCGTTAGTGGGAT[CG]CGCCTG TGAATAGCCACTGCCCTCCAGCCTGGGCAACAGCCAGACCCCGTCTGTTTAATA C Grn 148454441 + GeneID:57541 P51; P71; ZER6; KIAA1339; NM_020781.2 GI:25777702 isoform b is encoded by transcript variant 2; zinc finger DNA binding protein ZER6; zinc finger-estrogen receptor interaction; clone 6; zinc finger DNA binding protein p52/p71; go_component: nucleus; go_function: DNA binding; go_function: zinc ion binding; go_function: metal ion binding; go_function: transcriptional activator activity; go_process: transcription; go_process: regulation of transcription; DNA-dependent zinc finger 398 isoform b 671 TRUE 7:148453584-148455804 6 cg00007981 5260689 6860356 0.04542967 3554 8 23 408.7077 23.33452 3388 166 3.68E-38 PANX1 cg00007981 cg00007981 TOP 5260689 CCAAATTCAAAAAACTACAACTAAAACTAACTATAAACAAAATAATCACA 6860356 CCAAATTCAAAAAACTACGACTAAAACTAACTATAAACAAAATAATCACG 36 11 93502242 diploid Homo sapiens NCBI:RefSeq 36.1 BOT CCAAGTTCAAGGGGCTGCGACTGGAGCTGGCTGTGGACAAGATGGTCACG AGCCCACGGAGCCCAAGTTCAAGGGGCTGCGACTGGAGCTGGCTGTGGACAAGATGGTCA[CG]TGCATT GCGGTGGGGCTGCCCCTGCTGCTCATCTCGCTGGCCTTCGCGCAGGAGATCTCG T Red 93501742 + GeneID:24145 MRS1; UNQ2529; MGC21309; NM_015368.3 GI:39995063 innexin; go_component: membrane; go_component: gap junction; go_component: integral to membrane pannexin 1 500 TRUE 11:93501124-93502564 7 cg00008493 7200647 2900438 0.9610287 13782 16 26 37 1053.25 441 13341 3.68E-38 COX8C cg00008493 cg00008493 TOP 7200647 CTATCTACCACAATAAATTAAAACCCAACCATCATAATAAACAAAAAACA 2900438 CTATCTACCGCGATAAATTAAAACCCAACCATCATAATAAACGAAAAACG 36 14 92883530 diploid Homo sapiens NCBI:RefSeq 36.1 BOT CTGTCTGCCGCGGTGAGTTGAGGCCCAGCCATCATGGTGGGCGGGAAGCG CGCCAGCGGCCCCTGTCTGCCGCGGTGAGTTGAGGCCCAGCCATCATGGTGGGCGGGAAG[CG]CGTGGC CCTGGCGGGGCGCCCCGACGGGTGGGGAGAAGGGAGGACACGGCGTGCAGGCCT C Grn 92883290 + GeneID:341947 COX8-3; MGC119774; MGC119775; NM_182971.1 GI:33667031 cytochrome c oxidase subunit VIII isoform 3; go_component: mitochondrion; go_component: integral to membrane; go_component: organelle inner membrane; go_function: oxidoreductase activity; go_function: cytochrome-c oxidase activity; go_process: electron transport cytochrome c oxidase subunit 8C 240 TRUE 14:92883203-92883973 8 cg00008713 6860184 3780392 0.02229408 29280 17 17 909.5086 68.88012 28625 655 3.68E-38 IMPA2 cg00008713 cg00008713 TOP 6860184 CAAAACAATACAAAATTCTACACAAACCAAAAATAAAACCTATCTCAACA 3780392 CAAAACAATACGAAATTCTACACGAACCGAAAATAAAACCTATCTCAACG 36 18 11970953 diploid Homo sapiens NCBI:RefSeq 36.1 BOT CAGAACAGTACGGAGTTCTGCACGAGCCGGGGGTGGGGCCTGTCTCAGCG GCGCGCTTGACCCAGAACAGTACGGAGTTCTGCACGAGCCGGGGGTGGGGCCTGTCTCAG[CG]CGCGGC GGTGGGGCGGGGCTTGGACACGGGCCCGGCTCAACTTGAGGGAGGCGGGGCTCG C Grn 11971455 + GeneID:3613 NM_014214.1 GI:7657235 inosine monophosphatase 2; go_function: hydrolase activity; go_function: magnesium ion binding; go_function: inositol-1(or 4)-monophosphatase activity; go_process: signal transduction; go_process: phosphate metabolism inositol(myo)-1(or 4)-monophosphatase 2 502 TRUE 18:11970322-11972436 9 cg00009407 4230376 6380376 0.04024385 23357 19 21 1150.749 90.3898 22413 944 3.68E-38 TTC8 cg00009407 cg00009407 BOT 4230376 TAACCAAATTCTACTTACAATTATTTTTCTTTTTCCTATTCTCAAACACA 6380376 TAACCGAATTCTACTTACGATTATTTTTCTTTTTCCTATTCTCAAACGCG 36 14 88360674 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGCGCCTGAGAACAGGAAAAAGAAAAACAACCGCAAGCAGAACTCGGCTA GCGTCCGACTCTGCCCGGCAACCCGCGACGGCTGGGGCCTTGTCCGAGAGGTGCCCGCAG[CG]CGCCTG AGAACAGGAAAAAGAAAAACAACCGCAAGCAGAACTCGGCTACAGGGCTTGCCT C Grn 88360731 + GeneID:123016 BBS8; NM_198309.2 GI:53759117 isoform B is encoded by transcript variant 2; Bardet-Biedl syndrome type 8; go_function: binding; go_process: visual perception; go_process: sensory perception tetratricopeptide repeat domain 8 isoform B 57 TRUE 14:88360520-88361283 10 cg00010193 4780008 1580192 0.7163327 31934 18 24 895.9043 859.8419 8987 22947 3.68E-38 FLJ35816 cg00010193 cg00010193 BOT 4780008 AAATCAAAACAAACCTAAACACTATTACAACCTAACCAAATATACACACA 1580192 AAATCAAAACGAACCTAAACACTATTACAACCTAACCAAATATACACACG 36 4 1135216 diploid Homo sapiens NCBI:RefSeq 36.1 BOT AAGTCAGGGCGAGCCTGGGCACTGTTGCAGCCTGGCCAGGTGTGCACACG GATCTCAGAGTAAAGTCAGGGCGAGCCTGGGCACTGTTGCAGCCTGGCCAGGTGTGCACA[CG]CTCAGG GCAGTGCTAATACACCAGCCCCCTGCTGCCTCAGCACCCTCCAGACTTTAAGCA C Grn 1135160 + GeneID:401114 NM_207489.1 GI:46409601 hypothetical protein LOC401114 56 FALSE 11 cg00011459 3120296 7320368 0.8619227 2022 28 21 11.33893 86.55386 193 1829 9.89E-29 PMM2 cg00011459 cg00011459 TOP 3120296 AAAAATAATCTACTATCTCCCTTTCAAACTACCCTTCTCCAAACTATACA 7320368 AAAAATAATCTACTATCTCCCTTTCAAACTACCCTTCTCCGAACTATACG 36 16 8797926 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGCACAGCTCGGAGAAGGGCAGCCTGAAAGGGAGACAGTAGACCATTTCT CCACTGCAGCACCACAGCCCATGGAGAGGCCTTTCCCACACAGCTTTTCCCCGAAACCTA[CG]CACAGC TCGGAGAAGGGCAGCCTGAAAGGGAGACAGTAGACCATTTCTCTCATGGAACTC T Red 8799193 + GeneID:5373 CDG1; CDGS; CDG1a; NM_000303.1 GI:4557838 phosphomannomutase activity is deficient in patients with the carbohydrate-deficient glycoprotein syndrome type I (CDG1); go_component: cytoplasm; go_function: isomerase activity; go_function: phosphomannomutase activity; go_function: phosphomannomutase activity; go_process: metabolism; go_process: mannose biosynthesis; go_process: GDP-mannose biosynthesis; go_process: protein amino acid N-linked glycosylation phosphomannomutase 2 1267 FALSE 12 cg00012199 6200228 6200154 0.02216047 14295 16 14 970.5 16.25 13976 319 3.68E-38 RNASE4 cg00012199 cg00012199 BOT 6200228 AAAACTAAAACAATAAAACACACACAATTCTAACTACACAACTATAAACA 6200154 AAAACTAAAACGATAAAACGCACACAATTCTAACTACGCAACTATAAACG 36 14 20220864 diploid Homo sapiens NCBI:RefSeq 36.1 BOT GGGGCTGAGGCGGTGGGACGCACACAATTCTGACTGCGCAACTGTGAACG GTCGGAGAACTGGGGGCTGAGGCGGTGGGACGCACACAATTCTGACTGCGCAACTGTGAA[CG]CCGGAG AGGGCGGGCCTCCAGGCTTAGGCCCGGGCTCCCTGATGTCCTCACTTCCTGCGC C Grn 20222212 + GeneID:6038 RNS4; MGC9306; NM_194430.1 GI:37577169 go_component: cellular component unknown; go_function: hydrolase activity; go_function: nucleic acid binding; go_function: endonuclease activity; go_function: pancreatic ribonuclease activity; go_process: mRNA cleavage ribonuclease; RNase A family; 4 precursor 1348 TRUE 14:20220472-20221241 13 cg00012386 6840377 1510390 0.02178066 7751 22 12 406.5738 10.23363 7580 171 3.68E-38 C1orf142 cg00012386 cg00012386 BOT 6840377 AATTCAAATTATATTCCTAAACCCCACAATTTACAACTAATACAACCACA 1510390 AATTCGAATTATATTCCTAAACCCCACAATTTACAACTAATACAACCACG 36 1 225989135 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGTGGTTGTACCAGTTGCAAACTGTGGGGTCCAGGAATACAACTCGAACC GTTTGGAGTGAGGACGGGGCCCAGGGAGATGGCATGGACCGTGCCTTTCATTTCAGGAGA[CG]TGGTTG TACCAGTTGCAAACTGTGGGGTCCAGGAATACAACTCGAACCCCAAAGAGCACA T Red 225989320 + GeneID:116841 SVAP1; FLJ12517; IMAGE3451454; DKFZp686M10160; NM_053052.2 GI:26024192 synonyms: SVAP1; FLJ12517; IMAGE3451454; DKFZp686M10160 hypothetical protein LOC116841 185 TRUE 1:225989127-225990210 14 cg00012792 1340541 990678 0.02272532 11517 14 15 571.9391 39.82193 11253 264 3.68E-38 TXNDC5 cg00012792 cg00012792 BOT 1340541 AAAATAAAACTATACTAAAATCCACCAAAAACTATAACCCTAACACTCCA 990678 AAAATAAAACTATACTAAAATCCACCAAAAACTATAACCCTAACACTCCG 36 6 8009492 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGGAGTGTCAGGGCTATAGTTCCTGGTGGATCCCAGCACAGCCTCATCTC GCAGCAAGAAGAGGGACTCCCTGGGGACTGCGGGCTCAGCGCACCTCATTATCAAGGGTA[CG]GAGTGT CAGGGCTATAGTTCCTGGTGGATCCCAGCACAGCCTCATCTCCCAGGCGGCGCC T Red 8009596 - GeneID:81567 ERP46; UNQ364; EndoPDI; MGC3178; NM_030810.2 GI:42794770 isoform 1 is encoded by transcript variant 1; thioredoxin related protein; endothelial protein disulphide isomerase; go_component: endoplasmic reticulum; go_function: isomerase activity; go_function: electron transporter activity; go_process: anti- apoptosis; go_process: electron transport thioredoxin domain containing 5 isoform 1 104 TRUE 6:8008961-8009913 15 cg00013618 1410673 670594 0.8626667 16400 15 10 168.8621 385.2328 2166 14234 3.68E-38 cg00013618 cg00013618 BOT 1410673 CCCAAAACTATAATATTTAAAAATTCTCTACCCTCAAAAATCCCTAACCA 670594 CCCAAAACTATAATATTTAAAAATTCTCTACCCTCAAAAATCCCTAACCG 36 22 20710839 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGGTCAGGGATCCCTGAGGGCAGAGAATTTCCAAACATCACAGTTTTGGG TCAGGCTAGAGGCCCGAGATAGTCAGGGAGGCTGTGGTCCCAGACTTTGAGCCAGAGAAG[CG]GTCAGG GATCCCTGAGGGCAGAGAATTTCCAAACATCACAGTTTTGGGAGCACCGTGAGA C Grn 20710659 + GeneID:3535 180 FALSE 16 cg00014085 1240274 1780240 0.03166901 15562 22 30 832.3356 37.52333 15066 496 3.68E-38 RetSat cg00014085 cg00014085 BOT 1240274 ACCTTATTTAAAAACCTTCTTCCTAACCTCCTTATCAATTACCAAAAACA 1780240 ACCTTATTTAAAAACCTTCTTCCTAACCTCCTTATCAATTACCAAAAACG 36 2 85435016 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGCCCCTGGTAACTGACAAGGAGGCCAGGAAGAAGGTTCTCAAACAAGGT TGGGACTATTCTCTGGCAGCTCCCCGAATCCTTTCTCCGAAGATGTCAAACGGCCCCCAG[CG]CCCCTG GTAACTGACAAGGAGGCCAGGAAGAAGGTTCTCAAACAAGGTAGCAGGAGGGAC C Grn 85435166 - GeneID:54884 FLJ20296; NM_017750.2 GI:31377747 go_component: nuclear outer membrane; go_component: endoplasmic reticulum membrane; go_function: oxidoreductase activity; go_function: all-trans-retinol 13;14-reductase activity; go_process: electron transport; go_process: retinol metabolism all-trans-13;14-dihydroretinol saturase 150 TRUE 2:85434965-85435723 17 cg00014837 2970333 2190632 0.7356948 1001 21 22 15.92991 38.40635 191 810 0.000743657 ACRBP cg00014837 cg00014837 TOP 2970333 CCTTACATAATTACCATAAAAATCCCATAAAATAAATACACTATCATTCA 2190632 CCTTACGTAATTACCATAAAAATCCCATAAAATAAATACACTATCATTCG 36 12 6627518 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGAATGATAGTGTATCTACCTTATGGGATTCCTATGGCAATTACGTAAGG CCTCACGACCTGTTTGTTGGGCGAGTTGCTTCCCTAAGCCCCGATTTCTCATCTGTAAAA[CG]AATGAT AGTGTATCTACCTTATGGGATTCCTATGGCAATTACGTAAGGTAGTGCATGTAA T Red 6626841 - GeneID:84519 SP32; OY-TES-1; NM_032489.2 GI:17999523 go_component: cellular component unknown; go_function: molecular function unknown; go_process: biological process unknown proacrosin binding protein sp32 precursor 677 FALSE 18 cg00015770 50767 4730626 0.1244575 30087 21 15 1216.783 248.9866 26330 3757 3.68E-38 GPR103 cg00015770 cg00015770 BOT 50767 AAACATTTTTTAATCACTAAAATCAAATCTCCCAATACTTTAACTTCCCA 4730626 GAACATTTTTTAATCACTAAAATCGAATCTCCCAATACTTTAACTTCCCG 36 4 122521457 diploid Homo sapiens NCBI:RefSeq 36.1 BOT GAACATTTTTTGGTCACTGAGATCGAGTCTCCCAGTGCTTTGGCTTCCCG TATTTGAACCGCGAACATTTTTTGGTCACTGAGATCGAGTCTCCCAGTGCTTTGGCTTCC[CG]CCTCTT TATCGTGGGTTTGATCCCTGAGCTGCTCTCCTTTCCCGAACCTCCCGGGGTGCA C Grn 122521252 - GeneID:84109 AQ27; SP9155; NM_198179.1 GI:38016136 QRFP receptor; go_component: integral to membrane; go_function: receptor activity; go_function: neuropeptide Y receptor activity; go_function: rhodopsin-like receptor activity; go_process: signal transduction; go_process: G-protein coupled receptor protein signaling pathway G protein-coupled receptor 103 205 TRUE 4:122520698-122521834 19 cg00016968 5560324 5560008 0.8475475 27056 24 19 350.4812 1057.567 4040 23016 3.68E-38 RHOC cg00016968 cg00016968 BOT 5560324 TCTAAATCCCAACTATAAATTCTATTCCCACTCCTAAATCTAACTTAACA 5560008 TCTAAATCCCAACTATAAATTCTATTCCCACTCCTAAATCTAACTTAACG 36 1 113051971 diploid Homo sapiens NCBI:RefSeq 36.1 TOP CGCCAAGTCAGACCTAGGAGTGGGAACAGAATTCACAGCTGGGATCCAGA TCCCACCTCCTCAGCTCCCTTACAGGGAAAGGAGATACGCGTGTAGGTAAATATCCTATG[CG]CCAAGT CAGACCTAGGAGTGGGAACAGAATTCACAGCTGGGATCCAGAAGCATTTCTAGG C Grn 113051243 - GeneID:389 ARH9; ARHC; RHOH9; NM_175744.3 GI:34222243 Aplysia RAS-related homolog 9 (oncogene RHO H9); RAS homolog gene family; member C (oncogene RHO H9); Aplysia ras-related homolog 9; go_component: membrane; go_function: GTP binding; go_function: nucleotide binding; go_function: GTPase activity; go_function: signal transducer activity; go_process: small GTPase mediated signal transduction; go_process: positive regulation of I-kappaB kinase/NF-kappaB cascade ras homolog gene family; member C 728 FALSE Many thanks. Regards, Paul Pan Du wrote: > Hi Paul > > Please provide more detailed information, or else we cannot help you. > For example, please send me the returns of sessionInfo() and also the top > twenty lines of your data. I want to know whether it is because you are > using outdated packages or data in the wrong format. > Thanks! > > Pan > > > On 1/16/10 5:24 PM, "gilbert feng"<g-feng@northwestern.edu> wrote: > > >> From: Paul Sanfilippo<prseye@gmail.com> >> Date: Sun, 17 Jan 2010 10:16:41 +1100 >> To:<bioconductor@stat.math.ethz.ch> >> Subject: [BioC] lumiR error >> >> Dear List, >> >> I'm new to microarray analysis, so go easy. When I try to import some >> methylation data using lumiR, I receive the following error: >> >> >>> meth<-lumiR("~/desktop/meth_sample.txt") >>> >> Error in gregexpr("\t", dataLine1) : invalid 'text' argument >> >> If I specify "sep": >> >> >>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") >>> >> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : >> subscript out of bounds >> >> Does anyone know what might be causing the problem? Can lumiR handle >> this type of data where headers from BeadStudio are "..._Beta" instead >> of "..._Signal", etc >> >> Thank you, >> >> Paul Sanfilippo >> > > > -- > Pan Du, PhD > Research Assistant Professor > Northwestern University Biomedical Informatics Center > 750 N. Lake Shore Drive, 11-176 > Chicago, IL 60611 > Office (312) 503-2360; Fax: (312) 503-5388 > dupan (at) northwestern.edu > > > > > > [[alternative HTML version deleted]]
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Hi Paul Your data is Illumina Methylation data, not expression data. You need to use ³methylumi² package to preprocess the data. Actually, Sean Davis also told me this this morning. Pan On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye@gmail.com> wrote: > Hi Pan, > > I'm thinking the data is in the wrong format, but am keen to know if there's a > way around this (eg remapping column headers) > >> > sessionInfo() > R version 2.10.1 Patched (2009-12-29 r50852) > x86_64-apple-darwin9.8.0 > > locale: > [1] C/C/en_US/C/C/C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1 > [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 > [7] affy_1.24.2 annotate_1.24.1 AnnotationDbi_1.8.1 > [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2 > [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8 > [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2 > [19] rJava_0.8-1 > > loaded via a namespace (and not attached): > [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26 nlme_3.1-96 > [5] tools_2.10.1 xtable_1.5-6 >> > > > This is the data format that I have (I've just included the first subject > columns (in yellow)) > > > > Many thanks. > > Regards, > > Paul > > Pan Du wrote: >> >> Hi Paul >> >> Please provide more detailed information, or else we cannot help you. >> For example, please send me the returns of sessionInfo() and also the top >> twenty lines of your data. I want to know whether it is because you are >> using outdated packages or data in the wrong format. >> Thanks! >> >> Pan >> >> >> On 1/16/10 5:24 PM, "gilbert feng" <g-feng@northwestern.edu> >> <mailto:g-feng@northwestern.edu> wrote: >> >> >> >>> >>> From: Paul Sanfilippo <prseye@gmail.com> <mailto:prseye@gmail.com> >>> Date: Sun, 17 Jan 2010 10:16:41 +1100 >>> To: <bioconductor@stat.math.ethz.ch> <mailto:bioconductor@stat.math.ethz.ch> >>> Subject: [BioC] lumiR error >>> >>> Dear List, >>> >>> I'm new to microarray analysis, so go easy. When I try to import some >>> methylation data using lumiR, I receive the following error: >>> >>> >>> >>>> >>>> meth<-lumiR("~/desktop/meth_sample.txt") >>>> >>>> >>> >>> Error in gregexpr("\t", dataLine1) : invalid 'text' argument >>> >>> If I specify "sep": >>> >>> >>> >>>> >>>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") >>>> >>>> >>> >>> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : >>> subscript out of bounds >>> >>> Does anyone know what might be causing the problem? Can lumiR handle >>> this type of data where headers from BeadStudio are "..._Beta" instead >>> of "..._Signal", etc >>> >>> Thank you, >>> >>> Paul Sanfilippo >>> >>> >> >> [[alternative HTML version deleted]]
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Ok thanks. I thought I'd have a go with other packages as I hit a roadblock with methylumi in trying a normalisation. Thanks again for your help. Paul Pan Du wrote: > Hi Paul > > Your data is Illumina Methylation data, not expression data. You need > to use "methylumi" package to preprocess the data. > Actually, Sean Davis also told me this this morning. > > > Pan > > > On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye@gmail.com> wrote: > > Hi Pan, > > I'm thinking the data is in the wrong format, but am keen to know > if there's a way around this (eg remapping column headers) > > > sessionInfo() > R version 2.10.1 Patched (2009-12-29 r50852) > x86_64-apple-darwin9.8.0 > > locale: > [1] C/C/en_US/C/C/C > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1 > [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 > [7] affy_1.24.2 annotate_1.24.1 AnnotationDbi_1.8.1 > [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2 > [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8 > [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2 > [19] rJava_0.8-1 > > loaded via a namespace (and not attached): > [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26 > nlme_3.1-96 > [5] tools_2.10.1 xtable_1.5-6 > > > > This is the data format that I have (I've just included the first > subject columns (in yellow)) > > > > Many thanks. > > Regards, > > Paul > > Pan Du wrote: > > > Hi Paul > > Please provide more detailed information, or else we cannot > help you. > For example, please send me the returns of sessionInfo() and > also the top > twenty lines of your data. I want to know whether it is > because you are > using outdated packages or data in the wrong format. > Thanks! > > Pan > > > On 1/16/10 5:24 PM, "gilbert feng" <g-feng@northwestern.edu> > <mailto:g-feng@northwestern.edu> wrote: > > > > > From: Paul Sanfilippo <prseye@gmail.com> > <mailto:prseye@gmail.com> > Date: Sun, 17 Jan 2010 10:16:41 +1100 > To: <bioconductor@stat.math.ethz.ch> > <mailto:bioconductor@stat.math.ethz.ch> > Subject: [BioC] lumiR error > > Dear List, > > I'm new to microarray analysis, so go easy. When I try to > import some > methylation data using lumiR, I receive the following error: > > > > > meth<-lumiR("~/desktop/meth_sample.txt") > > > > Error in gregexpr("\t", dataLine1) : invalid 'text' argument > > If I specify "sep": > > > > > meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") > > > > Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : > subscript out of bounds > > Does anyone know what might be causing the problem? Can > lumiR handle > this type of data where headers from BeadStudio are > "..._Beta" instead > of "..._Signal", etc > > Thank you, > > Paul Sanfilippo > > > > [[alternative HTML version deleted]]
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On Mon, Jan 18, 2010 at 5:55 PM, Paul Sanfilippo <prseye at="" gmail.com=""> wrote: > Ok thanks. > > I thought I'd have a go with other packages as I hit a roadblock with > methylumi in trying a normalisation. Sorry, Paul. I have been busy and haven't gotten to looking at your problem. I hope to get to that in the next day or so. Sean > Pan Du wrote: >> Hi Paul >> >> Your data is Illumina Methylation data, not expression data. You need >> to use "methylumi" package to preprocess the data. >> Actually, Sean Davis also told me this this morning. >> >> >> Pan >> >> >> On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye at="" gmail.com=""> wrote: >> >> ? ? Hi Pan, >> >> ? ? I'm thinking the data is in the wrong format, but am keen to know >> ? ? if there's a way around this (eg remapping column headers) >> >> ? ? > sessionInfo() >> ? ? R version 2.10.1 Patched (2009-12-29 r50852) >> ? ? x86_64-apple-darwin9.8.0 >> >> ? ? locale: >> ? ? [1] C/C/en_US/C/C/C >> >> ? ? attached base packages: >> ? ? [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets >> ? ? methods >> ? ? [8] base >> >> ? ? other attached packages: >> ? ? ?[1] lumi_1.12.2 ? ? ? ? ?MASS_7.3-4 ? ? ? ? ? RSQLite_0.8-1 >> ? ? ?[4] DBI_0.2-5 ? ? ? ? ? ?preprocessCore_1.8.0 mgcv_1.6-1 >> ? ? ?[7] affy_1.24.2 ? ? ? ? ?annotate_1.24.1 ? ? ?AnnotationDbi_1.8.1 >> ? ? [10] Biobase_2.6.1 ? ? ? ?ggplot2_0.8.5 ? ? ? ?digest_0.4.2 >> ? ? [13] reshape_0.8.3 ? ? ? ?plyr_0.1.9 ? ? ? ? ? proto_0.3-8 >> ? ? [16] JGR_1.7-0 ? ? ? ? ? ?iplots_1.1-3 ? ? ? ? JavaGD_0.5-2 >> ? ? [19] rJava_0.8-1 >> >> ? ? loaded via a namespace (and not attached): >> ? ? [1] Matrix_0.999375-33 affyio_1.14.0 ? ? ?lattice_0.17-26 >> ? ? ? nlme_3.1-96 >> ? ? [5] tools_2.10.1 ? ? ? xtable_1.5-6 >> ? ? > >> >> ? ? This is the data format that I have (I've just included the first >> ? ? subject columns (in yellow)) >> >> >> >> ? ? Many thanks. >> >> ? ? Regards, >> >> ? ? Paul >> >> ? ? Pan Du wrote: >> >> >> ? ? ? ? Hi Paul >> >> ? ? ? ? Please provide more detailed information, or else we cannot >> ? ? ? ? help you. >> ? ? ? ? For example, please send me the returns of sessionInfo() and >> ? ? ? ? also the top >> ? ? ? ? twenty lines of your data. I want to know whether it is >> ? ? ? ? because you are >> ? ? ? ? using outdated packages or data in the wrong format. >> ? ? ? ? Thanks! >> >> ? ? ? ? Pan >> >> >> ? ? ? ? On 1/16/10 5:24 PM, "gilbert feng" <g-feng at="" northwestern.edu=""> >> ? ? ? ? <mailto:g-feng at="" northwestern.edu=""> ?wrote: >> >> >> >> >> ? ? ? ? ? ? From: Paul Sanfilippo <prseye at="" gmail.com=""> >> ? ? ? ? ? ? <mailto:prseye at="" gmail.com=""> >> ? ? ? ? ? ? Date: Sun, 17 Jan 2010 10:16:41 +1100 >> ? ? ? ? ? ? To: <bioconductor at="" stat.math.ethz.ch=""> >> ? ? ? ? ? ? <mailto:bioconductor at="" stat.math.ethz.ch=""> >> ? ? ? ? ? ? Subject: [BioC] lumiR error >> >> ? ? ? ? ? ? Dear List, >> >> ? ? ? ? ? ? I'm new to microarray analysis, so go easy. ?When I try to >> ? ? ? ? ? ? import some >> ? ? ? ? ? ? methylation data using lumiR, I receive the following error: >> >> >> >> >> ? ? ? ? ? ? ? ? meth<-lumiR("~/desktop/meth_sample.txt") >> >> >> >> ? ? ? ? ? ? Error in gregexpr("\t", dataLine1) : invalid 'text' argument >> >> ? ? ? ? ? ? If I specify "sep": >> >> >> >> >> ? ? ? ? ? ? ? ? meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") >> >> >> >> ? ? ? ? ? ? Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : >> ? ? ? ? ? ? ? ?subscript out of bounds >> >> ? ? ? ? ? ? Does anyone know what might be causing the problem? Can >> ? ? ? ? ? ? lumiR handle >> ? ? ? ? ? ? this type of data where headers from BeadStudio are >> ? ? ? ? ? ? "..._Beta" instead >> ? ? ? ? ? ? of "..._Signal", etc >> >> ? ? ? ? ? ? Thank you, >> >> ? ? ? ? ? ? Paul Sanfilippo >> >> >> >> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >
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No worries Sean. No pressure - I appreciate any help I can get. Regards, Paul Sean Davis wrote: > On Mon, Jan 18, 2010 at 5:55 PM, Paul Sanfilippo<prseye@gmail.com> wrote: > >> Ok thanks. >> >> I thought I'd have a go with other packages as I hit a roadblock with >> methylumi in trying a normalisation. >> > > Sorry, Paul. I have been busy and haven't gotten to looking at your > problem. I hope to get to that in the next day or so. > > Sean > > > >> Pan Du wrote: >> >>> Hi Paul >>> >>> Your data is Illumina Methylation data, not expression data. You need >>> to use "methylumi" package to preprocess the data. >>> Actually, Sean Davis also told me this this morning. >>> >>> >>> Pan >>> >>> >>> On 1/18/10 4:43 PM, "Paul Sanfilippo"<prseye@gmail.com> wrote: >>> >>> Hi Pan, >>> >>> I'm thinking the data is in the wrong format, but am keen to know >>> if there's a way around this (eg remapping column headers) >>> >>> > sessionInfo() >>> R version 2.10.1 Patched (2009-12-29 r50852) >>> x86_64-apple-darwin9.8.0 >>> >>> locale: >>> [1] C/C/en_US/C/C/C >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets >>> methods >>> [8] base >>> >>> other attached packages: >>> [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1 >>> [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 >>> [7] affy_1.24.2 annotate_1.24.1 AnnotationDbi_1.8.1 >>> [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2 >>> [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8 >>> [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2 >>> [19] rJava_0.8-1 >>> >>> loaded via a namespace (and not attached): >>> [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26 >>> nlme_3.1-96 >>> [5] tools_2.10.1 xtable_1.5-6 >>> > >>> >>> This is the data format that I have (I've just included the first >>> subject columns (in yellow)) >>> >>> >>> >>> Many thanks. >>> >>> Regards, >>> >>> Paul >>> >>> Pan Du wrote: >>> >>> >>> Hi Paul >>> >>> Please provide more detailed information, or else we cannot >>> help you. >>> For example, please send me the returns of sessionInfo() and >>> also the top >>> twenty lines of your data. I want to know whether it is >>> because you are >>> using outdated packages or data in the wrong format. >>> Thanks! >>> >>> Pan >>> >>> >>> On 1/16/10 5:24 PM, "gilbert feng"<g-feng@northwestern.edu> >>> <mailto:g-feng@northwestern.edu> wrote: >>> >>> >>> >>> >>> From: Paul Sanfilippo<prseye@gmail.com> >>> <mailto:prseye@gmail.com> >>> Date: Sun, 17 Jan 2010 10:16:41 +1100 >>> To:<bioconductor@stat.math.ethz.ch> >>> <mailto:bioconductor@stat.math.ethz.ch> >>> Subject: [BioC] lumiR error >>> >>> Dear List, >>> >>> I'm new to microarray analysis, so go easy. When I try to >>> import some >>> methylation data using lumiR, I receive the following error: >>> >>> >>> >>> >>> meth<-lumiR("~/desktop/meth_sample.txt") >>> >>> >>> >>> Error in gregexpr("\t", dataLine1) : invalid 'text' argument >>> >>> If I specify "sep": >>> >>> >>> >>> >>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t") >>> >>> >>> >>> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] : >>> subscript out of bounds >>> >>> Does anyone know what might be causing the problem? Can >>> lumiR handle >>> this type of data where headers from BeadStudio are >>> "..._Beta" instead >>> of "..._Signal", etc >>> >>> Thank you, >>> >>> Paul Sanfilippo >>> >>> >>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> [[alternative HTML version deleted]]
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