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 >> >> >> >> >> >> _______________________________________________ >> >> >> Bioconductor mailing list >> >> >> Bioconductor at r-project.org >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> Search the archives: >> >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> > >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >