Question: limma
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gravatar for João Fadista
12.9 years ago by
João Fadista500
João Fadista500 wrote:
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ADD COMMENTlink modified 12.9 years ago by Sean Davis21k • written 12.9 years ago by João Fadista500
Answer: limma
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gravatar for Sean Davis
12.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Monday 27 November 2006 11:28, Jo?o Fadista wrote: > Dear all, > > Does anybody know how can I remove values from an MAList? > I want to remove some values from a column in MA$genes dataframe, and > consequently remove those rows from MA$genes and MA$M. Subsetting works fine with MAList objects, I think. To remove the first five genes, you would do something like: MA[-c(1:5),] To remove the first five samples, you could do something like: MA[,-c(1:5)] In other words, rows are genes and columns are samples. Sean
ADD COMMENTlink written 12.9 years ago by Sean Davis21k
I usually do this using an indicator function. e.g. select=(eBayes.out$coef[,1]>1) # selects genes for which the first coef is bigger than 1 MA[select,] # is the set of genes for which select=T MA[!select,] # is the set of genes for which select=F --Naomi At 11:42 AM 11/27/2006, Sean Davis wrote: >On Monday 27 November 2006 11:28, Jo??o Fadista >wrote: > Dear all, > > Does anybody know how can >I remove values from an MAList? > I want to >remove some values from a column in MA$genes >dataframe, and > consequently remove those rows >from MA$genes and MA$M. Subsetting works fine >with MAList objects, I think. To remove the >first five genes, you would do something like: >MA[-c(1:5),] To remove the first five samples, >you could do something like: MA[,-c(1:5)] In >other words, rows are genes and columns are >samples. Sean >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
ADD REPLYlink written 12.9 years ago by Naomi Altman6.0k
It would be better to replace the unwanted elements with NA's rather than subset the structure, imageplot's for example will not work if the subsetted RGList or MAList is incomplete. e.g. MA$M[select,] <- NA Marcus On 11/28/06 6:19 AM, "Naomi Altman" <naomi at="" stat.psu.edu=""> wrote: > I usually do this using an indicator function. > > e.g. > select=(eBayes.out$coef[,1]>1) # > selects genes for which the first coef is bigger than 1 > > MA[select,] # is the set of genes for which select=T > MA[!select,] # is the set of genes for which select=F > > --Naomi > > > At 11:42 AM 11/27/2006, Sean Davis wrote: >> On Monday 27 November 2006 11:28, Jo??o Fadista >> wrote: > Dear all, > > Does anybody know how can >> I remove values from an MAList? > I want to >> remove some values from a column in MA$genes >> dataframe, and > consequently remove those rows >> from MA$genes and MA$M. Subsetting works fine >> with MAList objects, I think. To remove the >> first five genes, you would do something like: >> MA[-c(1:5),] To remove the first five samples, >> you could do something like: MA[,-c(1:5)] In >> other words, rows are genes and columns are >> samples. Sean >> _______________________________________________ >> 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 > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
ADD REPLYlink written 12.9 years ago by Marcus Davy680
Thanks a lot for all the reply messages. Best regards, Jo?o Fadista -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Marcus Davy Sent: 27 November 2006 23:39 To: Naomi Altman; sdavis2 at mail.nih.gov; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] limma It would be better to replace the unwanted elements with NA's rather than subset the structure, imageplot's for example will not work if the subsetted RGList or MAList is incomplete. e.g. MA$M[select,] <- NA Marcus On 11/28/06 6:19 AM, "Naomi Altman" <naomi at="" stat.psu.edu=""> wrote: > I usually do this using an indicator function. > > e.g. > select=(eBayes.out$coef[,1]>1) # > selects genes for which the first coef is bigger than 1 > > MA[select,] # is the set of genes for which select=T > MA[!select,] # is the set of genes for which select=F > > --Naomi > > > At 11:42 AM 11/27/2006, Sean Davis wrote: >> On Monday 27 November 2006 11:28, Jo??o Fadista >> wrote: > Dear all, > > Does anybody know how can I remove values from >> an MAList? > I want to remove some values from a column in MA$genes >> dataframe, and > consequently remove those rows from MA$genes and >> MA$M. Subsetting works fine with MAList objects, I think. To remove >> the first five genes, you would do something like: >> MA[-c(1:5),] To remove the first five samples, you could do something >> like: MA[,-c(1:5)] In other words, rows are genes and columns are >> samples. Sean _______________________________________________ >> 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 > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}} _______________________________________________ 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
ADD REPLYlink written 12.9 years ago by João Fadista500
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