If memory serves, the IDAT files for Illumina expression arrays are encrypted. A student here looked into this. For genotyping and Infinium methylation arrays, it is a solved problem (Keith Baggerly wrote the original code which Matt Ritchie adapted for the crlmm package, which I in turn adapted for methylumi, and more recently Kasper Daniel Hansen renovated the code yet again within crlmm to lay groundwork for the minfi package). My understanding is that the binary files from the expression arrays are not so easy to parse. On Mon, Oct 24, 2011 at 3:48 PM, Chintanu <chintanu@gmail.com> wrote: > Many thanks to Wei for providing the information. > > Vasu: Within GenePattern ( > http://genepattern.broadinstitute.org/gp/pages/login.jsf), use the module > called "IlluminaExpressionFileCreator" (help file's available here: > http://tinyurl.com/43n42et). This creates GCT files from a set of Illumina > expression IDAT files. The .gct files can then be used for any downstream > analysis. > > However, I am not sure how to do something similar in R to make use of the > .dat files. > Any comments welcome. > > Thank you. > > Cheers, > Chintanu > > ================================================== > > On Fri, Oct 21, 2011 at 5:59 PM, vasu punj <punjv@yahoo.com> wrote: > > > Chintanu, > > > > Would you specify the link with in Gene pattern which will use .idat > files > > please. > > Thanks. > > > > Vasu > > > > *From:* Chintanu <chintanu@gmail.com> > > *To:* Wei Shi <shi@wehi.edu.au> > > *Cc:* bioc <bioconductor@stat.math.ethz.ch> > > *Sent:* Thursday, October 20, 2011 10:35 PM > > > > *Subject:* Re: [BioC] Illumina array analysis > > > > Hello Wei, > > > > I have inherited these .idat files, and there seems to be no way that I > can > > get the text file(s) that you have mentioned. And, you say that I can no > > way > > make any use of these files using r, and is not a good news for me. > > > > However, I know that tools like GenePattern ( > > http://www.broadinstitute.org/cancer/software/genepattern/) uses .idat > > files; but I'm not sure whether similar to whatever process(es) being > > implemented at the backend of such tools can be deployed in r too !! > > Thank you. > > > > Cheers, > > Chintanu > > > > ================================================================== ====== > > On Wed, Oct 19, 2011 at 11:55 AM, Wei Shi <shi@wehi.edu.au> wrote: > > > > > Chintanu, > > > > > > The .idat files are only useful if you want to perform a bead- level > > > analysis (each probe contains around ~15-30 beads). But having .idat > > files > > > does not mean you have the complete bead-level data. You will have to > > have > > > .txt files in your data as well, which give the intensities for each > > bead. > > > But if the default setting of GenomeStudio/BeadStudio was used when > your > > > bead chips were scanned, these .txt file will NOT be outputted. This > > means > > > you can not perform a bead-level analysis even you have these .idat > > files. > > > > > > In most of the microarray experiments using Illumina bead chips, only > > > probe-level data are available. Limma starts the Illumina data analysis > > from > > > reading in the probe level data (read.ilmn function), performs neqc > > > normalization and then carry out differential expression analysis using > > > eBayes moderated t statistics (this step is the same for all different > > > microarray platforms). > > > > > > Hope this helps. > > > > > > Cheers, > > > Wei > > > > > > On Oct 19, 2011, at 11:41 AM, Chintanu wrote: > > > > > > Hi, > > > > > > Thanks to John, Wei, and Miles Pufall. > > > > > > While looking at your recommended documents/vignettes, I can't seem to > > find > > > any way of reading in the .idat files. In case of Affymetrix, the .cel > > files > > > can be easily read in using functions like ReadAffy() from Affy > package. > > For > > > spotted-arrays too, the .gpr files can be read easily. > > > > > > I have these .idat files that I'm hoping to analyse, but am unsure > > > regarding how I can read in the files, and (at the same time) can make > > use > > > of those recommended documents/vignettes. > > > > > > regards, > > > Chintanu > > > > > > ============================================================= > > > > > > > > >> > On Oct 18, 2011, at 12:55 PM, Chintanu wrote: > > >> > > > >> >> Hi, > > >> >> > > >> >> I'm new to my exploration with analysing illumina microarray data > > using > > >> r. > > >> >> While looking for some example case study (so that I can do my > > analysis > > >> >> taking pointers from that/those examples), I am unable to find > > anything > > >> >> useful. I would appreciate if you could either provide me with some > > >> pointers > > >> >> in that direction or share your codes that you have done while > doing > > >> your > > >> >> illumina analysis. > > >> >> > > >> >> I am mainly interested in the following: (i) read in the illumina > > files > > >> & > > >> >> check the quality of the files, (iii) normalization (any type), > (iii) > > >> >> applying Limma and pick the differentially expressed genes. > > >> >> > > >> >> Thank you. > > >> >> > > >> >> regards, > > >> >> Chintanu > > >> >> > > >> >> [[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 > > >> > > > >> > > > >> > > ______________________________________________________________________ > > >> > The information in this email is confidential and > > intend...{{dropped:9}} > > >> > > > >> > _______________________________________________ > > >> > 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 > > >> > > >> > > >> ______________________________________________________________________ > > >> The information in this email is confidential and intended solely for > > >> the addressee. > > >> You must not disclose, forward, print or use it without the permission > > of > > >> the sender. > > >> ______________________________________________________________________ > > >> > > > > > > > > > > > > ______________________________________________________________________ > > > The information in this email is confidential and inte...{{dropped:10}} > > > > > > _______________________________________________ > > 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]] > > _______________________________________________ > 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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]