Dear Nidhi, I've copied this onto the Bioconductor mailing list as we're now talking about a package from there, and it may be useful to others in the future to find this discussion. Can you please give me some more details as to how it is not working. If you could include the command you are running and any error messages that are produced, that would be great. Including the output from running the command sessionInfo() after you have encounter the problem will let me know exactly which versions of packages you are using. Thanks, Mike On 19/12/13 04:01, Nidhi Sharma wrote: Hello sir, I downloaded the illuminaio package, but this readIDAT command is still not working. On Wed, Dec 18, 2013 at 7:36 PM, Mike Smith <mike.smith@cruk.cam.ac.uk>wrote: > Dear Nidhi Sharma, > > Thanks for your interest in the IDATreader package. Are the data you're > working on from gene expression arrays? The file name below looks more > like those I've seen from SNP genotyping chips. IDATreader is designed > explicitly for expression arrays. > > Either way, you should take a look at the illuminaio package here: > http://www.bioconductor.org/packages/release/bioc/html/illuminaio.html > > All the code from IDATreader has been merged into that, so it should be > able to read any idat file you throw at it. > > illuminaio is just for extracting data. If you want to do some genotype > or copy number analysis you might want to consider using a package like > crlmm: > http://www.bioconductor.org/packages/2.13/bioc/html/crlmm.html > > Let me know if you have any more problems. > > Mike Smith > > > On 18/12/13 13:39, Nidhi Sharma wrote: > > Hello sir, > > I have installed the IDATreader and base64 package and other add- ons. When > I'm running the command using function to decrypt my file with .idat format > - > > idat <- readIDAT(file = "6164655051_R03C01_Red.idat") > > its showing error - Error in data[[i]] : subscript out of bounds > > I'm not able to solve this problem. Please guide me regarding this > problem. > > > > On Wed, Dec 18, 2013 at 6:07 PM, Nidhi Sharma <pg201384009@iitj.ac.in>wrote: > >> >> Hello sir, >> >> I have downloaded the IDATReader and base 64 package. I do have R >> already installed in my system. I want to know how can I install the >> IDATReader and base64 package. Please help me out asap. >> >> Regards, >> >> >> >> -- >> Nidhi Sharma >> PG201384009 >> PhD-BISS (I Year) >> IIT Jodhpur >> > > > > -- > Nidhi Sharma > PG201384009 > PhD-BISS (I Year) > IIT Jodhpur > > > -- Nidhi Sharma PG201384009 PhD-BISS (I Year) IIT Jodhpur [[alternative HTML version deleted]]

Nidhi, We are suspecting that the file is truncated; perhaps a bad download. Kasper On Thu, Dec 19, 2013 at 3:00 PM, Mike Smith <grimbough@gmail.com> wrote: > Dear Nidhi, > > I've copied this onto the Bioconductor mailing list as we're now talking > about a package from there, and it may be useful to others in the future to > find this discussion. > > Can you please give me some more details as to how it is not working. If > you could include the command you are running and any error messages that > are produced, that would be great. > > Including the output from running the command sessionInfo() after you have > encounter the problem will let me know exactly which versions of packages > you are using. > > Thanks, > Mike > > On 19/12/13 04:01, Nidhi Sharma wrote: > > Hello sir, > I downloaded the illuminaio package, but this readIDAT command is still not > working. > > > On Wed, Dec 18, 2013 at 7:36 PM, Mike Smith <mike.smith@cruk.cam.ac.uk> >wrote: > > > Dear Nidhi Sharma, > > > > Thanks for your interest in the IDATreader package. Are the data you're > > working on from gene expression arrays? The file name below looks more > > like those I've seen from SNP genotyping chips. IDATreader is designed > > explicitly for expression arrays. > > > > Either way, you should take a look at the illuminaio package here: > > http://www.bioconductor.org/packages/release/bioc/html/illuminaio.html > > > > All the code from IDATreader has been merged into that, so it should be > > able to read any idat file you throw at it. > > > > illuminaio is just for extracting data. If you want to do some genotype > > or copy number analysis you might want to consider using a package like > > crlmm: > > http://www.bioconductor.org/packages/2.13/bioc/html/crlmm.html > > > > Let me know if you have any more problems. > > > > Mike Smith > > > > > > On 18/12/13 13:39, Nidhi Sharma wrote: > > > > Hello sir, > > > > I have installed the IDATreader and base64 package and other add- ons. > When > > I'm running the command using function to decrypt my file with .idat > format > > - > > > > idat <- readIDAT(file = "6164655051_R03C01_Red.idat") > > > > its showing error - Error in data[[i]] : subscript out of bounds > > > > I'm not able to solve this problem. Please guide me regarding this > > problem. > > > > > > > > On Wed, Dec 18, 2013 at 6:07 PM, Nidhi Sharma <pg201384009@iitj.ac.in> >wrote: > > > >> > >> Hello sir, > >> > >> I have downloaded the IDATReader and base 64 package. I do have R > >> already installed in my system. I want to know how can I install the > >> IDATReader and base64 package. Please help me out asap. > >> > >> Regards, > >> > >> > >> > >> -- > >> Nidhi Sharma > >> PG201384009 > >> PhD-BISS (I Year) > >> IIT Jodhpur > >> > > > > > > > > -- > > Nidhi Sharma > > PG201384009 > > PhD-BISS (I Year) > > IIT Jodhpur > > > > > > > > > -- > Nidhi Sharma > PG201384009 > PhD-BISS (I Year) > IIT Jodhpur > > [[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 > [[alternative HTML version deleted]]