I think the file named:

GSE58037_meningiomas.raw.txt.gz

is the file with the data in it.  Again, since the illumina software allows
dumping for raw or normalized data, it is not clear what is actually in the
file and an email to authors may be required.

Sean



On Wed, Jul 23, 2014 at 11:58 AM, Abhishek Pratap <abhishek.vit@gmail.com>
wrote:

> Hi Sean
>
> I did download and open the files under raw data and strangely enough
> they have two files which seem like annotation for the Illumina
> probes.
>
>
> http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE58037&format=file&file=GSE58037%5Fmeningiomas%2Eraw%2Etxt%2Egz
>
> -A
>
> On Wed, Jul 23, 2014 at 8:52 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:
> > Hi, Abhi.
> >
> > It looks like the GSE record contains raw data.  However, you may need to
> > write to the authors to confirm what was done to create the .txt files
> that
> > are present in the raw data archives.
> >
> > Sean
> >
> >
> >
> > On Wed, Jul 23, 2014 at 11:43 AM, Abhishek Pratap <
> abhishek.vit@gmail.com>
> > wrote:
> >>
> >> Hi Sean
> >>
> >> Thanks for the details. I actually was wondering if I can get the raw
> >> data so I can do my own normalization. For example in the case of affy
> >> based GEO studies I normally see the raw CEL files also present which
> >> can be used with fRMA for producing normalized data.
> >>
> >> In this specific study
> >> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58037 I dont see
> >> the raw data similar to CEL files in affy studies. Just wondering if
> >> this particular case where that is missing or beadarray based studies
> >> dont tend to have raw data in GEO.
> >>
> >> Cheers!
> >> -Abhi
> >>
> >> On Wed, Jul 23, 2014 at 3:40 AM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
> >> >
> >> >
> >> >
> >> > On Thu, Jul 17, 2014 at 8:17 PM, Abhishek Pratap
> >> > <abhishek.vit@gmail.com>
> >> > wrote:
> >> >>
> >> >> Hi Guys
> >> >>
> >> >> I would like to know the basic analysis workflow for downloading and
> >> >> processing a Illumina HTV12 expression data from GEO. I have seen the
> >> >> beadArray vignette but not sure which normalization process to use.
> >> >>
> >> >> For example with Affy datasets I normally download the raw data and
> >> >> normalize it with fRMA package to produce a final expression matrix
> of
> >> >> genes.
> >> >>
> >> >> Here is some code but basically the final goal is to produce a
> >> >> normalized  expression matrix at genelevel.
> >> >>
> >> >> library( GEOquery )
> >> >> gse <- getGEO("GSE58037")
> >> >> gse <- gse[[1]]
> >> >> mat <- exprs(gse)
> >> >>
> >> >
> >> > Hi, Abhi.
> >> >
> >> > The "mat" variable above will give you expression measures as
> submitted
> >> > by
> >> > the authors.  NCBI GEO provides a description:
> >> >
> >> > "The data were normalised using normal-exponential convolution
> >> > model-based
> >> > background correction and quantile normalization. Merging of the data,
> >> > background removal and normalization processes were performed using
> the
> >> > limma R package. All of the batches were normalized at once after
> >> > excluding
> >> > probes with low quality."
> >> >
> >> > If you do not want to use those normalized values, then you will need
> to
> >> > define for yourself what the best approach is.  I don't know of an
> >> > accepted
> >> > "best" approach for such arrays.
> >> >
> >> > Sean
> >> >
> >> >
> >> >>
> >> >> Appreciate any pointers
> >> >>
> >> >> Thanks!
> >> >> -Abhi
> >> >>
> >> >> _______________________________________________
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> >> >
> >> >
> >>
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> >
> >
>
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