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Question: options on outputing gene expression based on gene level instead of probe set level for justRMA
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gravatar for Jack Luo
4.7 years ago by
Jack Luo340
Jack Luo340 wrote:
Hi, I am trying to RMA normalize a bunch of cel files and output the gene expression matrix to gene level (instead of probe set level), is there any option in justRMA that can do this (or any other function that can do this?) I searched the options on justRMA, does not seem to have this option. Thanks, -Jack [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.7 years ago by Peter Langfelder1.3k • written 4.7 years ago by Jack Luo340
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gravatar for James W. MacDonald
4.7 years ago by
United States
James W. MacDonald45k wrote:
Hi Jack, On 3/6/2013 11:48 AM, Jack Luo wrote: > Hi, > > I am trying to RMA normalize a bunch of cel files and output the gene A bunch of cel files of what Array type? > expression matrix to gene level (instead of probe set level), is there any > option in justRMA that can do this (or any other function that can do > this?) I searched the options on justRMA, does not seem to have this > option. > > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.7 years ago by James W. MacDonald45k
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gravatar for James W. MacDonald
4.7 years ago by
United States
James W. MacDonald45k wrote:
Please don't take things off list. On 3/6/2013 7:59 PM, Jack Luo wrote: > Gene 1.0 ST. At this point I guess I need to know what you mean by gene level. The affy package by definition only summarizes at the transcript level. But that doesn't mean that you only have one probeset per gene, as there may still be duplicates (splice variants or whatnot). If you just want a single expression value per gene, you can either use the genefilter package to subset by Entrez ID, or you could alternatively use one of the MBNI re-mapped cdf packages. Best, Jim > > On Wed, Mar 6, 2013 at 2:53 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Jack, > > > On 3/6/2013 11:48 AM, Jack Luo wrote: > > Hi, > > I am trying to RMA normalize a bunch of cel files and output > the gene > > > A bunch of cel files of what Array type? > > > expression matrix to gene level (instead of probe set level), > is there any > option in justRMA that can do this (or any other function that > can do > this?) I searched the options on justRMA, does not seem to > have this > option. > > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.7 years ago by James W. MacDonald45k
Thanks, Jim. That's very helpful. -Jack On Thu, Mar 7, 2013 at 8:57 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Please don't take things off list. > > On 3/6/2013 7:59 PM, Jack Luo wrote: > >> Gene 1.0 ST. >> > > At this point I guess I need to know what you mean by gene level. The affy > package by definition only summarizes at the transcript level. But that > doesn't mean that you only have one probeset per gene, as there may still > be duplicates (splice variants or whatnot). If you just want a single > expression value per gene, you can either use the genefilter package to > subset by Entrez ID, or you could alternatively use one of the MBNI > re-mapped cdf packages. > > Best, > > Jim > > > >> On Wed, Mar 6, 2013 at 2:53 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> Hi Jack, >> >> >> On 3/6/2013 11:48 AM, Jack Luo wrote: >> >> Hi, >> >> I am trying to RMA normalize a bunch of cel files and output >> the gene >> >> >> A bunch of cel files of what Array type? >> >> >> expression matrix to gene level (instead of probe set level), >> is there any >> option in justRMA that can do this (or any other function that >> can do >> this?) I searched the options on justRMA, does not seem to >> have this >> option. >> >> Thanks, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.7 years ago by Jack Luo340
0
gravatar for Peter Langfelder
4.7 years ago by
United States
Peter Langfelder1.3k wrote:
On Wed, Mar 6, 2013 at 8:48 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: > Hi, > > I am trying to RMA normalize a bunch of cel files and output the gene > expression matrix to gene level (instead of probe set level), is there any > option in justRMA that can do this (or any other function that can do > this?) I searched the options on justRMA, does not seem to have this > option. You can output probe-set level data, then use the function collapseRows in the WGCNA package (CRAN) to summarize probesets for each gene to a single value. Best, Peter
ADD COMMENTlink written 4.7 years ago by Peter Langfelder1.3k
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