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
>
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>
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