barcode support for other platforms
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Last seen 7.2 years ago
I am trying to assess whether genes in my samples are over expressed relative to a null mean. I use the barcode function in the R package frma for this purpose. As far as I understand the current Barcode version support only Affymetrix and only three platforms in it : GPL570, GPL96 and GPL1261. I do have other platforms. Do you happen to have mu null(and tau null) for other platforms? Do you know how can I do the same calculations for those as well? Thanks a lot, Romi -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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@matthew-mccall-4459
Last seen 2.4 years ago
United States
Romi, The barcode is now implemented on 5 platforms -- the 3 you mention plus GPL6244 and GPL6246. For other platforms, I would check out SCAN.UPC. Best, Matt On Sep 9, 2014 9:20 PM, "Romi Admanit [guest]" <guest at="" bioconductor.org=""> wrote: > I am trying to assess whether genes in my samples are over expressed > relative to a null mean. > I use the barcode function in the R package frma for this purpose. > As far as I understand the current Barcode version support only Affymetrix > and only three platforms in it : GPL570, GPL96 and GPL1261. > I do have other platforms. > Do you happen to have mu null(and tau null) for other platforms? > Do you know how can I do the same calculations for those as well? > Thanks a lot, > Romi > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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@w-evan-johnson-5447
Last seen 18 months ago
United States
Romi, Check the SCAN.UPC package and see if it has the functionalities you need. For more information check out our paper: http://www.pnas.org/content/110/44/17778.full Thanks! Evan On Sep 10, 2014, at 6:00 AM, bioconductor-request at r-project.org wrote: > Message: 15 > Date: Tue, 9 Sep 2014 18:20:50 -0700 (PDT) > From: "Romi Admanit [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, reuma at jimmy.harvard.edu > Subject: [BioC] barcode support for other platforms > Message-ID: <20140910012050.E643B60F1C at nutria.fhcrc.org> > > I am trying to assess whether genes in my samples are over expressed > relative to a null mean. > I use the barcode function in the R package frma for this purpose. > As far as I understand the current Barcode version support only Affymetrix > and only three platforms in it : GPL570, GPL96 and GPL1261. > I do have other platforms. > Do you happen to have mu null(and tau null) for other platforms? > Do you know how can I do the same calculations for those as well? > Thanks a lot, > Romi > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org.
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