standardized formats for RNAi screen datasets
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Rajarshi Guha ▴ 120
@rajarshi-guha-3531
Last seen 8.5 years ago
Hi, this is not a statistical question, but I am looking for standards governing exchange of RNAi screening datasets. I know that for DNA microarrays, MIAME exists. Is there something comparable for RNAi screening data? Thanks, -- Rajarshi Guha [[alternative HTML version deleted]]
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 10.2 years ago
http://mibbi.sourceforge.net/projects/MIARE/ (I'd also recommend you to browse the MIBBI pages; lots of interesting thoughts there) L. On Fri, 2009-08-14 at 10:09 -0400, Rajarshi Guha wrote: > Hi, this is not a statistical question, but I am looking for standards > governing exchange of RNAi screening datasets. I know that for DNA > microarrays, MIAME exists. Is there something comparable for RNAi screening > data? > > Thanks, >
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Hi, I don't know about the standards but the Bioconductor package, "cellHTS2" has a nice set up to store and process high throughput screening data. I have found it to be extremely useful. Check it out at http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html -Best -Lax On Fri, Aug 14, 2009 at 11:32 AM, Laurent Gautier <laurent@cbs.dtu.dk>wrote: > http://mibbi.sourceforge.net/projects/MIARE/ > > (I'd also recommend you to browse the MIBBI pages; lots of interesting > thoughts there) > > > L. > > On Fri, 2009-08-14 at 10:09 -0400, Rajarshi Guha wrote: > > Hi, this is not a statistical question, but I am looking for standards > > governing exchange of RNAi screening datasets. I know that for DNA > > microarrays, MIAME exists. Is there something comparable for RNAi > screening > > data? > > > > Thanks, > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Rajarshi, In addition to that...: While not a 'standard' (whatever that means), the reports generated by cellHTS2 (which include a number of raw data and metadata files) is what I and some colleagues perceive as a 'reasonable' format for dataset exchange. Note that 'data format' and 'minimal information about' are different things, one is an implementation, and one is conceptual. Best wishes Wolfgang Laurent Gautier wrote: > http://mibbi.sourceforge.net/projects/MIARE/ > > (I'd also recommend you to browse the MIBBI pages; lots of interesting > thoughts there) > > > L. > > On Fri, 2009-08-14 at 10:09 -0400, Rajarshi Guha wrote: >> Hi, this is not a statistical question, but I am looking for standards >> governing exchange of RNAi screening datasets. I know that for DNA >> microarrays, MIAME exists. Is there something comparable for RNAi screening >> data? >> >> Thanks, >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks for your comments. Being new to the field I was interested in looking for 'good practice' - obviously, working in R the cellHTS reports are the easiest way to go On Aug 17, 2009, at 4:30 PM, Wolfgang Huber wrote: > Hi Rajarshi, > > In addition to that...: > > While not a 'standard' (whatever that means), the reports generated > by cellHTS2 (which include a number of raw data and metadata files) > is what I and some colleagues perceive as a 'reasonable' format for > dataset exchange. > > Note that 'data format' and 'minimal information about' are > different things, one is an implementation, and one is conceptual. > > Best wishes > Wolfgang > > Laurent Gautier wrote: >> http://mibbi.sourceforge.net/projects/MIARE/ >> (I'd also recommend you to browse the MIBBI pages; lots of >> interesting >> thoughts there) >> L. >> On Fri, 2009-08-14 at 10:09 -0400, Rajarshi Guha wrote: >>> Hi, this is not a statistical question, but I am looking for >>> standards >>> governing exchange of RNAi screening datasets. I know that for DNA >>> microarrays, MIAME exists. Is there something comparable for RNAi >>> screening >>> data? >>> >>> Thanks, >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------------------------------------------- Rajarshi Guha <rajarshi.guha at="" gmail.com=""> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator.
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