Reading in mutiple files using readCtData
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Norm Allaire ▴ 50
@norm-allaire-6420
Last seen 10.2 years ago
Hi All, I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: >temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") The files I would like to read in are: ALS_Plate1_Rep1_Results_1361960062 ALS_Plate1_Rep2_Results_1361960064 ALS_Plate1_Rep3_Results_1361960066 ALS_Plate1_Rep4_Results_1361960068 ALS_Plate2_Rep1_Results_1361960063 ALS_Plate2_Rep2_Results_1361960065 ALS_Plate2_Rep3_Results_1361960067 ALS_Plate2_Rep4_Results_1361960069 Any help or suggestions would be greatly appreciated! Thanks so much, Norm Norm Allaire Scientist II Genetics and Genomics Biogen Idec 14 Cambridge Center Cambridge, MA 02142 Office: 617-679-2932 e-mail: norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com> [[alternative HTML version deleted]]
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@james-w-macdonald-5106
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Hi Norm, From ?readCtData: Arguments files character vector with the names of the files to be read. So are you asking if you can pass multiple files, or are you unsure how to make a character vector? Best, Jim On 2/26/2014 10:05 AM, Norm Allaire wrote: > Hi All, > > I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: >> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") > The files I would like to read in are: > > ALS_Plate1_Rep1_Results_1361960062 > ALS_Plate1_Rep2_Results_1361960064 > ALS_Plate1_Rep3_Results_1361960066 > ALS_Plate1_Rep4_Results_1361960068 > ALS_Plate2_Rep1_Results_1361960063 > ALS_Plate2_Rep2_Results_1361960065 > ALS_Plate2_Rep3_Results_1361960067 > ALS_Plate2_Rep4_Results_1361960069 > > Any help or suggestions would be greatly appreciated! > > Thanks so much, > > Norm > > > Norm Allaire > Scientist II > Genetics and Genomics > Biogen Idec > 14 Cambridge Center > Cambridge, MA 02142 > Office: 617-679-2932 > e-mail: norm.allaire at biogenidec.com<mailto:norm.allaire at="" biogenidec.com=""> > > [[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
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Hi Jim, Thanks for your help. The later, I don't know how to make a character vector. Norm -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Wednesday, February 26, 2014 10:46 AM To: Norm Allaire Cc: bioconductor at r-project.org Subject: Re: [BioC] Reading in mutiple files using readCtData Hi Norm, From ?readCtData: Arguments files character vector with the names of the files to be read. So are you asking if you can pass multiple files, or are you unsure how to make a character vector? Best, Jim On 2/26/2014 10:05 AM, Norm Allaire wrote: > Hi All, > > I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: >> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", >> path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = >> 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") > The files I would like to read in are: > > ALS_Plate1_Rep1_Results_1361960062 > ALS_Plate1_Rep2_Results_1361960064 > ALS_Plate1_Rep3_Results_1361960066 > ALS_Plate1_Rep4_Results_1361960068 > ALS_Plate2_Rep1_Results_1361960063 > ALS_Plate2_Rep2_Results_1361960065 > ALS_Plate2_Rep3_Results_1361960067 > ALS_Plate2_Rep4_Results_1361960069 > > Any help or suggestions would be greatly appreciated! > > Thanks so much, > > Norm > > > Norm Allaire > Scientist II > Genetics and Genomics > Biogen Idec > 14 Cambridge Center > Cambridge, MA 02142 > Office: 617-679-2932 > e-mail: > norm.allaire at biogenidec.com<mailto:norm.allaire at="" biogenidec.com=""> > > [[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
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Hi Norm, In that case you _really_ need to read An Introduction to R (http://cran.r-project.org/doc/manuals/R-intro.pdf). If you are getting hung up on the low-level fundamentals of R, you should at least get up to speed on the basics, as you are going nowhere until you do. Best, Jim On Wednesday, February 26, 2014 10:49:22 AM, Norm Allaire wrote: > Hi Jim, > > Thanks for your help. The later, I don't know how to make a character vector. > > Norm > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at uw.edu] > Sent: Wednesday, February 26, 2014 10:46 AM > To: Norm Allaire > Cc: bioconductor at r-project.org > Subject: Re: [BioC] Reading in mutiple files using readCtData > > Hi Norm, > > From ?readCtData: > > Arguments > files character vector with the names of the files > to be read. > > So are you asking if you can pass multiple files, or are you unsure how to make a character vector? > > Best, > > Jim > > > > On 2/26/2014 10:05 AM, Norm Allaire wrote: >> Hi All, >> >> I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: >>> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", >>> path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = >>> 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") >> The files I would like to read in are: >> >> ALS_Plate1_Rep1_Results_1361960062 >> ALS_Plate1_Rep2_Results_1361960064 >> ALS_Plate1_Rep3_Results_1361960066 >> ALS_Plate1_Rep4_Results_1361960068 >> ALS_Plate2_Rep1_Results_1361960063 >> ALS_Plate2_Rep2_Results_1361960065 >> ALS_Plate2_Rep3_Results_1361960067 >> ALS_Plate2_Rep4_Results_1361960069 >> >> Any help or suggestions would be greatly appreciated! >> >> Thanks so much, >> >> Norm >> >> >> Norm Allaire >> Scientist II >> Genetics and Genomics >> Biogen Idec >> 14 Cambridge Center >> Cambridge, MA 02142 >> Office: 617-679-2932 >> e-mail: >> norm.allaire at biogenidec.com<mailto:norm.allaire at="" biogenidec.com=""> >> >> [[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 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Norm, Just adding to Jim's comments, a character vector for your file names would look something like this: vec <- c("ALS_Plate1_Rep1_Results_1361960062", "ALS_Plate1_Rep2_Results_1361960064", "ALS_Plate1_Rep3_Results_1361960066", "ALS_Plate1_Rep4_Results_1361960068", "ALS_Plate2_Rep1_Results_1361960063", "ALS_Plate2_Rep2_Results_1361960065", "ALS_Plate2_Rep3_Results_1361960067", "ALS_Plate2_Rep4_Results_1361960069") The general syntax is c("char1", "char2"): > vec <- c("char1", "char2") > class(vec) [1] "character" Also this page <http: adv-r.had.co.nz="" data-structures.html=""> seems to have some good examples specifically of data structures in R. Kipper Fletez-Brant On Wed, Feb 26, 2014 at 10:49 AM, Norm Allaire <norm.allaire@biogenidec.com> wrote: > Hi Jim, > > Thanks for your help. The later, I don't know how to make a character > vector. > > Norm > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon@uw.edu] > Sent: Wednesday, February 26, 2014 10:46 AM > To: Norm Allaire > Cc: bioconductor@r-project.org > Subject: Re: [BioC] Reading in mutiple files using readCtData > > Hi Norm, > > From ?readCtData: > > Arguments > files character vector with the names of the files > to be read. > > So are you asking if you can pass multiple files, or are you unsure how to > make a character vector? > > Best, > > Jim > > > > On 2/26/2014 10:05 AM, Norm Allaire wrote: > > Hi All, > > > > I'm new to R. I just installed the HTqPCR package and I'm trying to > create a qPCRset object from 8 Fluidigm files. I got some help earlier to > read in one file but now I need to read in the whole set. Also, when I read > in the single file the sample names were listed as 1.file name, 2.file name > etc. and I would like to know how to specify the correct names that are in > the file. The previous command I used was: > >> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", > >> path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = > >> 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") > > The files I would like to read in are: > > > > ALS_Plate1_Rep1_Results_1361960062 > > ALS_Plate1_Rep2_Results_1361960064 > > ALS_Plate1_Rep3_Results_1361960066 > > ALS_Plate1_Rep4_Results_1361960068 > > ALS_Plate2_Rep1_Results_1361960063 > > ALS_Plate2_Rep2_Results_1361960065 > > ALS_Plate2_Rep3_Results_1361960067 > > ALS_Plate2_Rep4_Results_1361960069 > > > > Any help or suggestions would be greatly appreciated! > > > > Thanks so much, > > > > Norm > > > > > > Norm Allaire > > Scientist II > > Genetics and Genomics > > Biogen Idec > > 14 Cambridge Center > > Cambridge, MA 02142 > > Office: 617-679-2932 > > e-mail: > > norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > On Wed, Feb 26, 2014 at 10:58 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Norm, > > In that case you _really_ need to read An Introduction to R ( > http://cran.r-project.org/doc/manuals/R-intro.pdf). If you are getting > hung up on the low-level fundamentals of R, you should at least get up to > speed on the basics, as you are going nowhere until you do. > > Best, > > Jim > > > > On Wednesday, February 26, 2014 10:49:22 AM, Norm Allaire wrote: > >> Hi Jim, >> >> Thanks for your help. The later, I don't know how to make a character >> vector. >> >> Norm >> >> -----Original Message----- >> From: James W. MacDonald [mailto:jmacdon@uw.edu] >> Sent: Wednesday, February 26, 2014 10:46 AM >> To: Norm Allaire >> Cc: bioconductor@r-project.org >> Subject: Re: [BioC] Reading in mutiple files using readCtData >> >> Hi Norm, >> >> From ?readCtData: >> >> Arguments >> files character vector with the names of the files >> to be read. >> >> So are you asking if you can pass multiple files, or are you unsure how >> to make a character vector? >> >> Best, >> >> Jim >> >> >> >> On 2/26/2014 10:05 AM, Norm Allaire wrote: >> >>> Hi All, >>> >>> I'm new to R. I just installed the HTqPCR package and I'm trying to >>> create a qPCRset object from 8 Fluidigm files. I got some help earlier to >>> read in one file but now I need to read in the whole set. Also, when I read >>> in the single file the sample names were listed as 1.file name, 2.file name >>> etc. and I would like to know how to specify the correct names that are in >>> the file. The previous command I used was: >>> >>>> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", >>>> path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = >>>> 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") >>>> >>> The files I would like to read in are: >>> >>> ALS_Plate1_Rep1_Results_1361960062 >>> ALS_Plate1_Rep2_Results_1361960064 >>> ALS_Plate1_Rep3_Results_1361960066 >>> ALS_Plate1_Rep4_Results_1361960068 >>> ALS_Plate2_Rep1_Results_1361960063 >>> ALS_Plate2_Rep2_Results_1361960065 >>> ALS_Plate2_Rep3_Results_1361960067 >>> ALS_Plate2_Rep4_Results_1361960069 >>> >>> Any help or suggestions would be greatly appreciated! >>> >>> Thanks so much, >>> >>> Norm >>> >>> >>> Norm Allaire >>> Scientist II >>> Genetics and Genomics >>> Biogen Idec >>> 14 Cambridge Center >>> Cambridge, MA 02142 >>> Office: 617-679-2932 >>> e-mail: >>> norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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 Kipper, Thanks again for the second time in as many days! Your advice has been really helpful. Cheers, Norm From: Kipper Fletez-Brant [mailto:cafletezbrant@gmail.com] Sent: Wednesday, February 26, 2014 11:01 AM To: James W. MacDonald Cc: Norm Allaire; bioconductor@r-project.org Subject: Re: [BioC] Reading in mutiple files using readCtData Norm, Just adding to Jim's comments, a character vector for your file names would look something like this: vec <- c("ALS_Plate1_Rep1_Results_1361960062", "ALS_Plate1_Rep2_Results_1361960064", "ALS_Plate1_Rep3_Results_1361960066", "ALS_Plate1_Rep4_Results_1361960068", "ALS_Plate2_Rep1_Results_1361960063", "ALS_Plate2_Rep2_Results_1361960065", "ALS_Plate2_Rep3_Results_1361960067", "ALS_Plate2_Rep4_Results_1361960069") The general syntax is c("char1", "char2"): > vec <- c("char1", "char2") > class(vec) [1] "character" Also this page<http: adv-r.had.co.nz="" data-structures.html=""> seems to have some good examples specifically of data structures in R. Kipper Fletez-Brant On Wed, Feb 26, 2014 at 10:49 AM, Norm Allaire <norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com>> wrote: Hi Jim, Thanks for your help. The later, I don't know how to make a character vector. Norm -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu<mailto:jmacdon@uw.edu>] Sent: Wednesday, February 26, 2014 10:46 AM To: Norm Allaire Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] Reading in mutiple files using readCtData Hi Norm, From ?readCtData: Arguments files character vector with the names of the files to be read. So are you asking if you can pass multiple files, or are you unsure how to make a character vector? Best, Jim On 2/26/2014 10:05 AM, Norm Allaire wrote: > Hi All, > > I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: >> temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", >> path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = >> 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") > The files I would like to read in are: > > ALS_Plate1_Rep1_Results_1361960062 > ALS_Plate1_Rep2_Results_1361960064 > ALS_Plate1_Rep3_Results_1361960066 > ALS_Plate1_Rep4_Results_1361960068 > ALS_Plate2_Rep1_Results_1361960063 > ALS_Plate2_Rep2_Results_1361960065 > ALS_Plate2_Rep3_Results_1361960067 > ALS_Plate2_Rep4_Results_1361960069 > > Any help or suggestions would be greatly appreciated! > > Thanks so much, > > Norm > > > Norm Allaire > Scientist II > Genetics and Genomics > Biogen Idec > 14 Cambridge Center > Cambridge, MA 02142 > Office: 617-679-2932 > e-mail: > norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com><mail to:norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com="">> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor On Wed, Feb 26, 2014 at 10:58 AM, James W. MacDonald <jmacdon@uw.edu<mailto:jmacdon@uw.edu>> wrote: Hi Norm, In that case you _really_ need to read An Introduction to R (http://cran.r-project.org/doc/manuals/R-intro.pdf). If you are getting hung up on the low-level fundamentals of R, you should at least get up to speed on the basics, as you are going nowhere until you do. Best, Jim On Wednesday, February 26, 2014 10:49:22 AM, Norm Allaire wrote: Hi Jim, Thanks for your help. The later, I don't know how to make a character vector. Norm -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu<mailto:jmacdon@uw.edu>] Sent: Wednesday, February 26, 2014 10:46 AM To: Norm Allaire Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] Reading in mutiple files using readCtData Hi Norm, From ?readCtData: Arguments files character vector with the names of the files to be read. So are you asking if you can pass multiple files, or are you unsure how to make a character vector? Best, Jim On 2/26/2014 10:05 AM, Norm Allaire wrote: Hi All, I'm new to R. I just installed the HTqPCR package and I'm trying to create a qPCRset object from 8 Fluidigm files. I got some help earlier to read in one file but now I need to read in the whole set. Also, when I read in the single file the sample names were listed as 1.file name, 2.file name etc. and I would like to know how to specify the correct names that are in the file. The previous command I used was: temp <- readCtData(files = "ALS_Plate1_Rep1_Results_1361960062.csv", path = "C:/Users/allairen/R/Fluidigm", n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",") The files I would like to read in are: ALS_Plate1_Rep1_Results_1361960062 ALS_Plate1_Rep2_Results_1361960064 ALS_Plate1_Rep3_Results_1361960066 ALS_Plate1_Rep4_Results_1361960068 ALS_Plate2_Rep1_Results_1361960063 ALS_Plate2_Rep2_Results_1361960065 ALS_Plate2_Rep3_Results_1361960067 ALS_Plate2_Rep4_Results_1361960069 Any help or suggestions would be greatly appreciated! Thanks so much, Norm Norm Allaire Scientist II Genetics and Genomics Biogen Idec 14 Cambridge Center Cambridge, MA 02142 Office: 617-679-2932<tel:617-679-2932> e-mail: norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com><mailto :norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com="">> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> 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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