Question: PAMR- Package: Workflow and/or other methods
0
gravatar for Peter Kupfer
6.8 years ago by
Peter Kupfer70
Peter Kupfer70 wrote:
Dear all, i searched for a classification method for microarrays with 3 groups. Therefore I found the package "PAMR" which works out for the example data and with the tutorial ( http://www- stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html ) Well, i tried it with my data and the output is not so good as expected. So I asked myself if there is any limitation regarding the numbers of genes for the input . Are there any experiences regarding the input/gene numbers? If there are any methods/scripts for classification of three diseases, please let me know. All the best and thanks Peter
classification • 1.3k views
ADD COMMENTlink modified 6.8 years ago by Sean Davis21k • written 6.8 years ago by Peter Kupfer70
Answer: PAMR- Package: Workflow and/or other methods
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gravatar for Sean Davis
6.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Nov 19, 2012 at 10:11 AM, Peter Kupfer <peter.kupfer@me.com> wrote: > Dear all, > i searched for a classification method for microarrays with 3 groups. > Therefore I found the package "PAMR" which works out for the example data > and with the tutorial ( > http://www-stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html ) > Well, i tried it with my data and the output is not so good as expected. > So I asked myself if there is any limitation regarding the numbers of genes > for the input . Are there any experiences regarding the input/gene numbers? > > If there are any methods/scripts for classification of three diseases, > please let me know. > There are MANY. However, you might take a look at this package to get started: http://bioconductor.org/packages/release/bioc/html/MLInterfaces.html Sean > All the best and thanks > Peter > > _______________________________________________ > 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]]
ADD COMMENTlink written 6.8 years ago by Sean Davis21k
Thanks Sean, but i guess: The included methods are not so different to methods in the e1071-package. I guess: For thousands of genes it is a little bit difficult or? Maybe I have to choose an other method. You suggest one? Thanks Peter Am 19.11.2012 um 16:29 schrieb Sean Davis <sdavis2@mail.nih.gov>: > > > > On Mon, Nov 19, 2012 at 10:11 AM, Peter Kupfer <peter.kupfer@me.com> wrote: > Dear all, > i searched for a classification method for microarrays with 3 groups. Therefore I found the package "PAMR" which works out for the example data and with the tutorial ( http://www- stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html ) > Well, i tried it with my data and the output is not so good as expected. So I asked myself if there is any limitation regarding the numbers of genes for the input . Are there any experiences regarding the input/gene numbers? > > If there are any methods/scripts for classification of three diseases, please let me know. > > There are MANY. However, you might take a look at this package to get started: > > http://bioconductor.org/packages/release/bioc/html/MLInterfaces.html > > Sean > > > All the best and thanks > Peter > > _______________________________________________ > 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]]
ADD REPLYlink written 6.8 years ago by Peter Kupfer70
You might want to look into the 'CMA' Bioconductor package or the 'bootfs' package on CRAN if classification is your goal. On Mon, Nov 19, 2012 at 11:41 AM, Peter Kupfer <peter.kupfer@me.com> wrote: > Thanks Sean, > but i guess: The included methods are not so different to methods in the > e1071-package. I guess: For thousands of genes it is a little bit difficult > or? Maybe I have to choose an other method. You suggest one? > Thanks > Peter > > > Am 19.11.2012 um 16:29 schrieb Sean Davis <sdavis2@mail.nih.gov>: > > > > > > > > > On Mon, Nov 19, 2012 at 10:11 AM, Peter Kupfer <peter.kupfer@me.com> > wrote: > > Dear all, > > i searched for a classification method for microarrays with 3 groups. > Therefore I found the package "PAMR" which works out for the example data > and with the tutorial ( > http://www-stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html ) > > Well, i tried it with my data and the output is not so good as expected. > So I asked myself if there is any limitation regarding the numbers of genes > for the input . Are there any experiences regarding the input/gene numbers? > > > > If there are any methods/scripts for classification of three diseases, > please let me know. > > > > There are MANY. However, you might take a look at this package to get > started: > > > > http://bioconductor.org/packages/release/bioc/html/MLInterfaces.html > > > > Sean > > > > > > All the best and thanks > > Peter > > > > _______________________________________________ > > 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]] > > _______________________________________________ > 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 > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Tim Triche4.2k
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