how to set up sampleInfo for methylation array in illumina 450K
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Guest User ★ 12k
@guest-user-4897
Last seen 8.1 years ago
Dear Users, I tried to use lumi to import the methylation array data from illumina 450k array into R using lumi package, but I could not find the instruction on how to format the sampleInfo file. I just set it as below: SENTRIX_ID SENTRIX_BARCODE SENTRIX_POSITION Group ART initiation Infection 01A00421_NR056388 8691803116 R01C01 HIV-CTR N None 01A00068_NR056389 8691803116 R02C01 HIV-CTR N None 01A00483_NR056390 8691803116 R03C01 HIV-CTR N None 01A00347_NR056391 8691803116 R04C01 HIV-CTR N None 01A00060_NR056393 8691803116 R05C01 Medium N Pre 01A00065_NR056395 8691803116 R06C01 Medium N Post 01A00113_NR056404 8691803116 R01C02 Medium N Post 01A00079_NR056406 8691803116 R02C02 Medium N Post After reading the sampleinfo file using read.csv() as below sampleInfo=read.csv("sampleInfo_12.csv",sep="\t",header=T,stringsAsFac tors=F) I used the function as instructed in the turtorial My_data=importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix=FALSE, dir.bigMatrix='.') There is an error message: Error in importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix = FALSE, : 'SENTRIX_POSITION' and 'SENTRIX_BARCODE' or 'SENTRIX_ID' and are required in 'sampleInfo'! I don't get it that I already added those required items in the sampleInfo, why does it have this error? Thanks a lot for the help and I really appreciate it. -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) 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] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.14.2 BiocInstaller_1.12.1 VariantAnnotation_1.8.13 Rsamtools_1.14.3 Biostrings_2.30.1 GenomicRanges_1.14.4 [7] XVector_0.2.0 IRanges_1.20.7 ggplot2_0.9.3.1 phyloseq_1.6.1 picante_1.6-2 nlme_3.1-117 [13] ape_3.1-1 ade4_1.6-2 knitr_1.5 vegan_2.0-10 lattice_0.20-29 permute_0.8-3 [19] biom_0.3.12 metagenomeSeq_1.5.47 devtools_1.5 gplots_2.13.0 RColorBrewer_1.0-5 matrixStats_0.8.14 [25] limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1 beanplot_1.1 [7] biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 bumphunter_1.2.0 caTools_1.17 cluster_1.15.2 [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 doRNG_1.6 [19] evaluate_0.5.3 foreach_1.4.2 formatR_0.10 gdata_2.13.3 genefilter_1.44.0 GenomicFeatures_1.14.5 [25] grid_3.0.2 gtable_0.1.2 gtools_3.4.0 httr_0.3 igraph_0.7.1 illuminaio_0.4.0 [31] iterators_1.0.7 itertools_0.1-3 KernSmooth_2.23-12 labeling_0.2 locfit_1.5-9.1 MASS_7.3-31 [37] Matrix_1.1-3 mclust_4.3 memoise_0.2.1 methylumi_2.8.0 mgcv_1.7-29 minfi_1.8.9 [43] multtest_2.18.0 munsell_0.4.2 nleqslv_2.1.1 nor1mix_1.1-4 pkgmaker_0.20 plyr_1.8.1 [49] preprocessCore_1.24.0 proto_0.3-10 R.methodsS3_1.6.1 Rcpp_0.11.1 RCurl_1.95-4.1 registry_0.2 [55] reshape_0.8.5 reshape2_1.4 RJSONIO_1.2-0.1 rngtools_1.2.4 RSQLite_0.11.4 rtracklayer_1.22.7 [61] scales_0.2.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [67] tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 xtable_1.7-3 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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Pan Du ▴ 440
@pan-du-4636
Last seen 8.1 years ago
Hi I guess you didn't input the sampleInfo correctly. Based on your filename "sampleInfo_12.csv", it is a csv file, not a Tab delimited file. So try to import the file using read.csv function. I also noticed there are "SENTRIX_ID" columns together with "SENTRIX_BARCODE" and "SENTRIX_POSITION". The importMethyIDAT function assumes the "SENTRIX_ID" is a combination of "SENTRIX_BARCODE" and "SENTRIX_POSITION". But looks like your data does not meet this assumption. So please remove the "SENTRIX_ID" column. Tell me if the problem still exists. Pan On Tue, Apr 29, 2014 at 10:29 AM, guest [guest] <guest@bioconductor.org>wrote: > > Dear Users, > > I tried to use lumi to import the methylation array data from illumina > 450k array into R using lumi package, but I could not find the instruction > on how to format the sampleInfo file. I just set it as below: > > SENTRIX_ID SENTRIX_BARCODE SENTRIX_POSITION Group ART > initiation Infection > 01A00421_NR056388 8691803116 R01C01 HIV-CTR N None > 01A00068_NR056389 8691803116 R02C01 HIV-CTR N None > 01A00483_NR056390 8691803116 R03C01 HIV-CTR N None > 01A00347_NR056391 8691803116 R04C01 HIV-CTR N None > 01A00060_NR056393 8691803116 R05C01 Medium N Pre > 01A00065_NR056395 8691803116 R06C01 Medium N Post > 01A00113_NR056404 8691803116 R01C02 Medium N Post > 01A00079_NR056406 8691803116 R02C02 Medium N Post > > After reading the sampleinfo file using read.csv() as below > > sampleInfo=read.csv("sampleInfo_12.csv",sep="\t",header=T,stringsAsF actors=F) > > I used the function as instructed in the turtorial > My_data=importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, > bigMatrix=FALSE, dir.bigMatrix='.') > > There is an error message: > Error in importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, > bigMatrix = FALSE, : > 'SENTRIX_POSITION' and 'SENTRIX_BARCODE' or 'SENTRIX_ID' and are > required in 'sampleInfo'! > > I don't get it that I already added those required items in the > sampleInfo, why does it have this error? > > Thanks a lot for the help and I really appreciate it. > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.2 (2013-09-25) > 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] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] lumi_2.14.2 BiocInstaller_1.12.1 > VariantAnnotation_1.8.13 Rsamtools_1.14.3 Biostrings_2.30.1 > GenomicRanges_1.14.4 > [7] XVector_0.2.0 IRanges_1.20.7 ggplot2_0.9.3.1 > phyloseq_1.6.1 picante_1.6-2 nlme_3.1-117 > [13] ape_3.1-1 ade4_1.6-2 knitr_1.5 > vegan_2.0-10 lattice_0.20-29 permute_0.8-3 > [19] biom_0.3.12 metagenomeSeq_1.5.47 devtools_1.5 > gplots_2.13.0 RColorBrewer_1.0-5 matrixStats_0.8.14 > [25] limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.1 > AnnotationDbi_1.24.0 base64_1.1 beanplot_1.1 > [7] biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 > bumphunter_1.2.0 caTools_1.17 cluster_1.15.2 > [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > dichromat_2.0-0 digest_0.6.4 doRNG_1.6 > [19] evaluate_0.5.3 foreach_1.4.2 formatR_0.10 > gdata_2.13.3 genefilter_1.44.0 GenomicFeatures_1.14.5 > [25] grid_3.0.2 gtable_0.1.2 gtools_3.4.0 > httr_0.3 igraph_0.7.1 illuminaio_0.4.0 > [31] iterators_1.0.7 itertools_0.1-3 KernSmooth_2.23-12 > labeling_0.2 locfit_1.5-9.1 MASS_7.3-31 > [37] Matrix_1.1-3 mclust_4.3 memoise_0.2.1 > methylumi_2.8.0 mgcv_1.7-29 minfi_1.8.9 > [43] multtest_2.18.0 munsell_0.4.2 nleqslv_2.1.1 > nor1mix_1.1-4 pkgmaker_0.20 plyr_1.8.1 > [49] preprocessCore_1.24.0 proto_0.3-10 R.methodsS3_1.6.1 > Rcpp_0.11.1 RCurl_1.95-4.1 registry_0.2 > [55] reshape_0.8.5 reshape2_1.4 RJSONIO_1.2-0.1 > rngtools_1.2.4 RSQLite_0.11.4 rtracklayer_1.22.7 > [61] scales_0.2.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 stringr_0.6.2 survival_2.37-7 > [67] tools_3.0.2 whisker_0.3-2 XML_3.95-0.2 > xtable_1.7-3 zlibbioc_1.8.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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