Question: prepare data matrix for siggenes
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gravatar for joseph
8.5 years ago by
joseph330
joseph330 wrote:
I am preparing data matrix for siggenes as follow: data=read.table("data.txt", skip=1, header = F) data=as.matrix(data) data[1:3, ] V1 V2 V3 V4 V5 V6 V7 V8 [1,] 0.26 0.21 0.37 0.47 0.43 0.35 0.15 0.50 [2,] 0.21 0.22 0.40 0.40 0.28 0.23 0.17 0.40 is it ok to have the defualt column names? if not, how can I suppess it when I use read.table? Thank you Joseph [[alternative HTML version deleted]]
siggenes • 575 views
ADD COMMENTlink modified 8.5 years ago by Holger Schwender900 • written 8.5 years ago by joseph330
Answer: prepare data matrix for siggenes
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gravatar for Holger Schwender
8.5 years ago by
Holger Schwender900 wrote:
siggenes does not care about how you call the columns of your matrix. So both sam and ebam should work. Holger -------- Original-Nachricht -------- > Datum: Mon, 4 Apr 2011 10:57:11 -0700 (PDT) > Von: joseph <jdsandjd at="" yahoo.com=""> > An: bioconductor at r-project.org > Betreff: [BioC] prepare data matrix for siggenes > I am preparing data matrix for siggenes as follow: > > data=read.table("data.txt", skip=1, header = F) > data=as.matrix(data) > data[1:3, ] > > V1 V2 V3 V4 V5 V6 V7 V8 > [1,] 0.26 0.21 0.37 0.47 0.43 0.35 0.15 0.50 > [2,] 0.21 0.22 0.40 0.40 0.28 0.23 0.17 0.40 > > is it ok to have the defualt column names? if not, how can I suppess it > when I > use read.table? > Thank you > Joseph > [[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 -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl
ADD COMMENTlink written 8.5 years ago by Holger Schwender900
Hi Holger I got an Warning message when I used the data: > sam.out = sam(sumis, cl, rand = 123, gene.names = sumis.names, var.equal = >TRUE) We're doing 70 complete permutations Warning message: There are 2 variables with zero variance. These variables are removed, and their d-values are set to NA. how serious is this warning, and how can I identify the 2 variables with zero variance? thanks Joseph ________________________________ From: Holger Schwender <holger.schw@gmx.de> Sent: Mon, April 4, 2011 12:09:53 PM Subject: Re: [BioC] prepare data matrix for siggenes siggenes does not care about how you call the columns of your matrix. So both sam and ebam should work. Holger -------- Original-Nachricht -------- > Datum: Mon, 4 Apr 2011 10:57:11 -0700 (PDT) > An: bioconductor@r-project.org > Betreff: [BioC] prepare data matrix for siggenes > I am preparing data matrix for siggenes as follow: > > data=read.table("data.txt", skip=1, header = F) > data=as.matrix(data) > data[1:3, ] > > V1 V2 V3 V4 V5 V6 V7 V8 > [1,] 0.26 0.21 0.37 0.47 0.43 0.35 0.15 0.50 > [2,] 0.21 0.22 0.40 0.40 0.28 0.23 0.17 0.40 > > is it ok to have the defualt column names? if not, how can I suppess it > when I > use read.table? > Thank you > Joseph > [[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 -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl [[alternative HTML version deleted]]
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