Hi Mike, Thank you so much for your advice. I can now install it properly and succeeded to read a idat file. After I read a idat file, then it contains information something like following. > idat[1:10,] MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData BackgroundDevBinData CodesBinData NumBeadsBinData 1 577.37201 586.94641 102.94595 563.49585 0 0 10008 21 2 105.32843 107.54086 17.36357 102.84825 0 0 10010 18 3 105.47916 106.90141 23.27995 98.20106 0 0 10014 26 4 96.03654 97.22727 12.01887 93.85848 0 0 10017 18 5 101.15079 102.46756 14.26707 102.40277 0 0 10019 21 6 110.97807 111.94042 15.54425 108.54636 0 0 10020 25 7 93.36533 94.80687 12.88733 91.90852 0 0 10021 17 8 103.91557 105.35213 19.37169 102.13950 0 0 10025 22 9 105.39189 106.81569 12.94761 107.72005 0 0 10026 19 10 100.90147 102.46033 18.38206 93.95204 0 0 10035 16 NumGoodBeadsBinData IllumicodeBinData 1 20 10008 2 18 10010 3 26 10014 4 17 10017 5 20 10019 6 23 10020 7 16 10021 8 21 10025 9 19 10026 10 16 10035 This is my first time to analyze gene expression of idat file, so please let me ask a few naive questions. 1) Is CodesBinData (which is identical with IllumicodeBinData here) same as probe ID? 2) What value would be compared with other samples as gene expression level? MeanBinData or TrimmedMeanBinData? 3) It this data processed or pre-processed (i.e background correction or normalization)? 4) Is there any other known package I can work on from this point to proceed analysis? Thank you so much for your help. Best regards, Seungyeul On Aug 25, 2012, at 3:12 PM, Mike Smith 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 > 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 [[alternative HTML version deleted]]