Hi Seungyeul, Thanks for the bug report. This boiled down to the probeID setting not working, which i've now fixed. ConvertNuID is not a valid parameter to lumiR.idat, since I now provide more probe-naming options via probeID, specifically, setting probeID="NuID" does the same thing as lumiR(..., ConvertNuID=TRUE, ...) As for naming rows by Entrez ID's, you can do this by using the BioC annotation packages from Mark Dunning. eg library(illuminaHumanv4.db) # and specifically, the illuminaHumanv4ENTREZID object # hint: Lkeys(illuminaHumanv4ENTREZID)[1:10] [1] "ILMN_1343048" "ILMN_1343049" "ILMN_1343050" "ILMN_1343052" "ILMN_1343059" [6] "ILMN_1343061" "ILMN_1343062" "ILMN_1343063" "ILMN_1343064" "ILMN_1343291" Rkeys(illuminaHumanv4ENTREZID)[1:10] [1] "1" "2" "3" "9" "10" "11" "12" "13" "14" "15" cheers, Mark On 01/09/2012, at 6:35 AM, Yoo, Seungyeul wrote: > Dear Mark, > > Thanks for sharing "lumidat" package with me. I think it works fine now. But I'm wondering if an argument "convertNuID" is available in lumiR.idat(). When I ran it it failed with error like following. > > > res<-lumiR.idat(filenames,manifestfile="HumanHT- 12_V4_0_R1_15002873_B.txt",na.rm=TRUE,probeID="NuID",convertNuID=TRUE) > java -Xmx1024m -jar /Library/Frameworks/R.framework/Versions/2.15/Re sources/library/lumidat/bin/IlluminaGeneExpressionIdatReader-1.0.jar -outputDir /var/folders/q6/hny37vrd5wx_77gpj71ng3cw0000gn/T//RtmpHnCFD6 -bg false -collapse none -manifestfile HumanHT-12_V4_0_R1_15002873_B.txt '8473515005_A_Grn.idat' '8473515005_B_Grn.idat' '8473515005_C_Grn.idat' '8473515005_D_Grn.idat' '8473515005_E_Grn.idat' '8473515005_F_Grn.idat' '8473515005_G_Grn.idat' '8473515005_H_Grn.idat' '8473515005_I_Grn.idat' '8473515005_J_Grn.idat' '8473515005_K_Grn.idat' '8473515005_L_Grn.idat' > iDAT files: [8473515005_A_Grn.idat, 8473515005_B_Grn.idat, 8473515005_C_Grn.idat, 8473515005_D_Grn.idat, 8473515005_E_Grn.idat, 8473515005_F_Grn.idat, 8473515005_G_Grn.idat, 8473515005_H_Grn.idat, 8473515005_I_Grn.idat, 8473515005_J_Grn.idat, 8473515005_K_Grn.idat, 8473515005_L_Grn.idat] > Wrote: Sample Probe Profile.txt > Wrote: Control Probe Profile.txt > Error in lumiR(files[1], detectionTh = detectionTh, na.rm = na.rm, convertNuID = FALSE, : > formal argument "convertNuID" matched by multiple actual arguments > > If I remove convertNuID=TRUE, it works fine but featureNames are defined by ProbeID. > > After I read this I want to play with matrix generated by "exprs()" and rownames is always same with probeID. > > There is an another argument in lumiR.idat, probeID. However, there is no changes when I select ProbeID or NuID. > > I want the rownames are NuID or EntrezID at the end. And can you please let me know how I can do it? > > Best regards, > > Seungyeul Yoo > > Postdoctoral Fellow > Jun Zhu's Laboratory > Institute of Genomics and Multiscale Biology > Department of Genetics and Genomic Sciences > Mount Sinai School of Medicine > (office) 212-659-6877 > > > > > On Aug 27, 2012, at 8:40 PM, Mark Cowley wrote: > >> Dear all, >> I have been developing 'lumidat' which provides equivalents to lumi::lumiR and limma::read.ilmn which accept idat files. There's no compiled code (java handles the decryption), so it's easy to install on linux or mac. >> I've used it on hundreds of arrays, so please contact me if you're interested in testing it out. >> >> cheers, >> Mark >> >> On 28/08/2012, at 9:20 AM, Kasper Daniel Hansen wrote: >> >>> You / we / someone should consider wrapping this into a more easy to >>> install package, together with crlmm::readIDAT (and in case there are >>> other Illumina parsing functions around, they could be included as >>> well). What is the license for openssl? >>> >>> Kasper >>> >>> On Sat, Aug 25, 2012 at 3:12 PM, Mike Smith <grimbough@gmail.com> wrote: >>>> Hi Seungyeul, >>>> >>>> IDATreader's a pretty experimental package, but it's worked on the few >>>> systems I've tested it on. The reliance on third party libraries is >>>> why I've not submitted it to Bioconductor, so they may be causing >>>> problems. >>>> >>>> I'm not sure why you're using source(), rather than loading the >>>> package via library(). Have you installed the package, or just >>>> unzipped it and grabbed the .R file? It need to be installed in order >>>> to build the DLL and link against the decryption routines. To do that >>>> you need to download the tar.gz from the website you linked to and >>>> then run >>>> >>>> R CMD INSTALL IDATreader_0.1.1.tar.gz >>>> >>>> in a terminal to installed the package. You then need to load it using >>>> >>>> library(IDATreader) >>>> >>>> in your R session, rather than using source(). >>>> >>>> Hopefully that's of some help, >>>> >>>> Mike >>>> >>>> >>>> >>>> On 22 August 2012 23:35, Yoo, Seungyeul <seungyeul.yoo@mssm.edu> wrote: >>>>> Hi all, >>>>> >>>>> I'm trying to analyze Illumina array of gene expression. The file format is .idat which is encrypted data. >>>>> >>>>> I downloaded IDATreader packages as Mike suggested in some of previous post. I also install openssl for my mac os x. http://www.compbio.group.cam.ac.uk/software/idatreader >>>>> >>>>> But when I tried to read idat file error message is prompted. >>>>> >>>>> source("/Library/R/readIDAT.R") >>>>> filenames<-dir(patter="idat") >>>>> idat<-readIDAT(file=filenames[1]) >>>>> >>>>>> idat<-readIDAT(file=filenames[1]) >>>>> Decrypting to XML >>>>> Error in .C("decryptSSL", as.character(file), as.character(tempFile), : >>>>> C symbol name "decryptSSL" not in DLL for package "IDATreader" >>>>> >>>>>> sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: i386-apple-darwin9.8.0/i386 (32-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] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] BiocInstaller_1.4.7 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.15.0 >>>>> >>>>> Please let me have any advices to solve this problem. >>>>> >>>>> Seungyeul Yoo >>>>> >>>>> Postdoctoral Fellow >>>>> Jun Zhu's Laboratory >>>>> Institute of Genomics and Multiscale Biology >>>>> Department of Genetics and Genomic Sciences >>>>> Mount Sinai School of Medicine >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> -- >>>> Mike Smith >>>> PhD Student >>>> Computational Biology Group >>>> Cambridge University >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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]]