[BioC] processing Illumina HT12v4.0 expression data from GEO

[Abhishek Pratap]

Thanks Sean. I guess if I need to dig deeper I will have to follow up
with authors. For now I will just explore the normalized data that is
present at GEO.


Cheers!
-Abhi

On Wed, Jul 23, 2014 at 9:06 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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 at 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 at 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 at 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 at mail.nih.gov>
>> >> wrote:
>> >> >
>> >> >
>> >> >
>> >> > On Thu, Jul 17, 2014 at 8:17 PM, Abhishek Pratap
>> >> > <abhishek.vit at 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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