Question: how to set up sampleInfo for methylation array in illumina 450K
0
gravatar for Guest User
5.0 years ago by
Guest User12k
Guest User12k 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,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.
lumi • 925 views
ADD COMMENTlink modified 5.0 years ago by Pan Du440 • written 5.0 years ago by Guest User12k
Answer: how to set up sampleInfo for methylation array in illumina 450K
0
gravatar for Pan Du
5.0 years ago by
Pan Du440
Pan Du440 wrote:
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]]
ADD COMMENTlink written 5.0 years ago by Pan Du440
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 151 users visited in the last hour