Hi, I've been trying to read in Illumina's *.idat file to no success. Both of my data are from this platform:- Illumina HumanHT-12 V3.0 expression beadchip I suspect that this may be caused by the version of R that I am using and so has switched from R version 3.0.1 (2013-05-16) -- "Good Sport" to R version 2.10.1 (2009-12-14) to see if it works but the same error persist. This is the sample of my dataset from GSE21973_non-normalized.txt:- D_REF HSC rep1 Detection Pval HSC rep2 Detection Pval HSC rep3 Detection Pval MPP rep1 Detection Pval MPP rep2 Detection Pval MPP rep3 Detection Pval MLP rep1 Detection Pval MLP rep2 Detection Pval MLP rep3 Detection Pval CMP rep1 Detection Pval CMP rep2 Detection Pval CMP rep3 Detection Pval GMP rep1 Detection Pval GMP rep2 Detection Pval MEP rep1 Detection Pval MEP rep2 Detection Pval ILMN_1910180 136.4 0.12253 116.6 0.55468 133.3 0.19368 115.9 0.42951 122.2 0.33202 141.8 0.07905 161.4 0.05138 119 0.5336 129.9 0.3386 128.5 0.11726 123.1 0.31225 131.6 0.31884 142 0.1581 159.4 0.10013 162.2 0.07115 137.8 0.27009 ILMN_1725881 164.9 0.01713 168.8 0.01186 141.9 0.09486 110.7 0.62187 161.5 0.01713 172.6 0.01054 211.5 0.00659 143.1 0.04743 170.7 0.00527 143.4 0.02767 166.1 0.01845 154 0.06983 198.2 0.00395 200.6 0.01581 169.4 0.0448 146.7 0.13307 ILMN_1804174 141.1 0.08169 140.4 0.05929 126.8 0.33465 124.7 0.17523 143.3 0.05665 128.4 0.22793 157.1 0.07115 141.7 0.05665 130 0.3386 120 0.31094 140.8 0.07246 157.5 0.05402 151.2 0.06588 135.4 0.51383 142.4 0.2859 132.1 0.40053 These are the codes and errors from R:- > require(lumi) Loading required package: lumi Loading required package: annotate Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affy Loading required package: mgcv This is mgcv 1.6-1. For overview type `help("mgcv-package")'. Loading required package: preprocessCore Loading required package: RSQLite Loading required package: DBI Loading required package: MASS > lumiR("GSM513193_4674281056_L_Grn.idat") Error in gregexpr("\t", dataLine1) : invalid 'text' argument In addition: Warning message: In readLines(fileName, n = 20) : incomplete final line found on 'GSM513193_4674281056_L_Grn.idat' > lumiR("GSE21973_non-normalized.txt") Error in gregexpr("\t", dataLine1) : invalid 'text' argument Can you please advise me on which packages to install for it to work? Thanks. -- output of sessionInfo(): > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.12.4 MASS_7.3-4 RSQLite_0.9-2 DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 affy_1.24.2 [8] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26 Matrix_0.999375-33 nlme_3.1-96 tools_2.10.1 xtable_1.5-6 -- Sent via the guest posting facility at bioconductor.org.

If you are trying to analyse data from GEO, it might be best to use the Geoquery package. The data could have been pre-processed before uploading, so no longer in the standard format that lumi expects. You will not be able to read idat files in lumi. Best wishes, Mark On Thursday, June 13, 2013, Joanne [guest] <guest@bioconductor.org> wrote: > > Hi, > > I've been trying to read in Illumina's *.idat file to no success. > > Both of my data are from this platform:- > Illumina HumanHT-12 V3.0 expression beadchip > > I suspect that this may be caused by the version of R that I am using and so has switched from R version 3.0.1 (2013-05-16) -- "Good Sport" to R version 2.10.1 (2009-12-14) to see if it works but the same error persist. > > This is the sample of my dataset from GSE21973_non-normalized.txt:- > D_REF HSC rep1 Detection Pval HSC rep2 Detection Pval HSC rep3 Detection Pval MPP rep1 Detection Pval MPP rep2 Detection Pval MPP rep3 Detection Pval MLP rep1 Detection Pval MLP rep2 Detection Pval MLP rep3 Detection Pval CMP rep1 Detection Pval CMP rep2 Detection Pval CMP rep3 Detection Pval GMP rep1 Detection Pval GMP rep2 Detection Pval MEP rep1 Detection Pval MEP rep2 Detection Pval > ILMN_1910180 136.4 0.12253 116.6 0.55468 133.3 0.19368 115.9 0.42951 122.2 0.33202 141.8 0.07905 161.4 0.05138 119 0.5336 129.9 0.3386 128.5 0.11726 123.1 0.31225 131.6 0.31884 142 0.1581 159.4 0.10013 162.2 0.07115 137.8 0.27009 > ILMN_1725881 164.9 0.01713 168.8 0.01186 141.9 0.09486 110.7 0.62187 161.5 0.01713 172.6 0.01054 211.5 0.00659 143.1 0.04743 170.7 0.00527 143.4 0.02767 166.1 0.01845 154 0.06983 198.2 0.00395 200.6 0.01581 169.4 0.0448 146.7 0.13307 > ILMN_1804174 141.1 0.08169 140.4 0.05929 126.8 0.33465 124.7 0.17523 143.3 0.05665 128.4 0.22793 157.1 0.07115 141.7 0.05665 130 0.3386 120 0.31094 140.8 0.07246 157.5 0.05402 151.2 0.06588 135.4 0.51383 142.4 0.2859 132.1 0.40053 > > These are the codes and errors from R:- > >> require(lumi) > Loading required package: lumi > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affy > Loading required package: mgcv > This is mgcv 1.6-1. For overview type `help("mgcv-package")'. > Loading required package: preprocessCore > Loading required package: RSQLite > Loading required package: DBI > Loading required package: MASS > >> lumiR("GSM513193_4674281056_L_Grn.idat") > Error in gregexpr("\t", dataLine1) : invalid 'text' argument > In addition: Warning message: > In readLines(fileName, n = 20) : > incomplete final line found on 'GSM513193_4674281056_L_Grn.idat' >> lumiR("GSE21973_non-normalized.txt") > Error in gregexpr("\t", dataLine1) : invalid 'text' argument > > Can you please advise me on which packages to install for it to work? > > Thanks. > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_1.12.4 MASS_7.3-4 RSQLite_0.9-2 DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1 affy_1.24.2 > [8] annotate_1.24.1 AnnotationDbi_1.8.2 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26 Matrix_0.999375-33 nlme_3.1-96 tools_2.10.1 xtable_1.5-6 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]