Question

permutation

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Peevi Ijkl ▴ 170

@peevi-ijkl-4360

Last seen 9.6 years ago

Hi I am trying to do a permutation with a p cut off of 0.05 from a dataset and generate pathways.can someone tell me how to do it thanks peevi [[alternative HTML version deleted]]

Pathways Pathways • 760 views

ADD COMMENT • link updated 13.4 years ago by Steve Lianoglou ★ 13k • written 13.4 years ago by Peevi Ijkl ▴ 170

score 0 · Answer 1 · 2010-12-02

Hi, On Thu, Dec 2, 2010 at 1:05 AM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > Hi > I am trying to do a permutation with a p cut off of 0.05 from a dataset and > generate pathways.can someone tell me how to do it I'm guessing that'd be unlikely without more information from you. What are you permuting? What type of data is in your dataset? What type of pathways are you looking for? What have you tried to do already? -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

score 0 · Answer 2 · 2010-12-02

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 13 months ago

United States

Hi Peevi, Please keep all correspondence on the list as other people will be the ones helping you with this. Your response is below: On Thu, Dec 2, 2010 at 2:46 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > hello steve > this is wot i did so far.. > load the cel files..gcRMA..nonspecific filtering..then GeneSetCollection foe > KEGG..constructed an incidence matrix..computed per gene test statistics > using rowttest function..Compute the Z score for ?each pathway..now i want > to do permutation using library(Category) and list pathways with p value cut > off? .05 . But sorry .. I'm not really sure what you're trying to do, and can't spend much time trying to. I was hoping your exposition would provide more information that others can use to help you with. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 13.4 years ago Steve Lianoglou ★ 13k

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Hi Peevi, On 12/2/2010 2:51 PM, Steve Lianoglou wrote: > Hi Peevi, > > Please keep all correspondence on the list as other people will be the > ones helping you with this. > > Your response is below: > > On Thu, Dec 2, 2010 at 2:46 PM, Peevi Ijkl<ipeevi at="" yahoo.com=""> wrote: >> hello steve >> this is wot i did so far.. >> load the cel files..gcRMA..nonspecific filtering..then GeneSetCollection foe >> KEGG..constructed an incidence matrix..computed per gene test statistics >> using rowttest function..Compute the Z score for each pathway..now i want >> to do permutation using library(Category) and list pathways with p value cut >> off .05 . I believe this is covered on page 7 of the Category vignette: http://www.bioconductor.org/packages/2.7/bioc/vignettes/Category/inst/ doc/Category.pdf Best, Jim > > But sorry .. I'm not really sure what you're trying to do, and can't > spend much time trying to. > > I was hoping your exposition would provide more information that > others can use to help you with. > > -steve > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD REPLY • link 13.4 years ago James W. MacDonald 65k