Is there any way to get M-values in topTable?

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@prashantha-hebbar-kiradi-mu-mlsc-3159

Last seen 10.2 years ago

Dear Friends, I want to know, is there in possibility to get M- values instead of log fold change value (logFC) in tapTable command used in LIMMA package? In case "yes", Please let me know how to do it? Thanking you in anticipation. Regards, Prashantha ###################################################################### Attention:\ This e-mail message is privileged and confid...{{dropped:10}}

limma limma • 1.1k views

ADD COMMENT • link updated 15.9 years ago by James W. MacDonald 67k • written 15.9 years ago by Prashantha Hebbar Kiradi [MU-MLSC] ▴ 90

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 13 hours ago

United States

Hi Prashantha, M-values _are_ log fold changes, so the default of limma is to supply these data. IIRC, topTable() previously labeled this column 'M', but Gordon changed that a couple of years ago (or so). Best, Jim Prashantha Hebbar wrote: > Dear Friends, > > > > I want to know, is there in possibility to get M- values instead of log fold > change value (logFC) in tapTable command used in LIMMA package? In case > "yes", Please let me know how to do it? > > > > Thanking you in anticipation. > > > > Regards, > > > > Prashantha > > > ###################################################################### > Attention:\ This e-mail message is privileged and confid...{{dropped:10}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

ADD COMMENT • link 15.9 years ago James W. MacDonald 67k

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Hi, I was wondering if there are tools available for following purposes when working with genome-wide association (GWA) analysis: - Power calculations for continuous traits when using non-familial data - Joint analysis of continuous traits (significance and effect size) when combining results from GWAS and replication studies. All help is greatly appreciated! Best, Jussi

ADD REPLY • link 15.9 years ago Jussi Paananen ▴ 20

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Hello, I am currently working on a power calculator that may be what you are looking for. A first release is already available. Please check this link: https://www.msu.edu/~steibelj/JP_files/QpowR.html Feel free to email me off-list with questions. Feedback is greatly appreciated Cheers, JP Jussi Paananen wrote: > Hi, > > I was wondering if there are tools available for following purposes > when working with genome-wide association (GWA) analysis: > > - Power calculations for continuous traits when using non-familial data > - Joint analysis of continuous traits (significance and effect size) > when combining results from GWAS and replication studies. > > All help is greatly appreciated! > > Best, > Jussi > > _______________________________________________ > 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 > > -- ============================= Juan Pedro Steibel Assistant Professor Statistical Genetics and Genomics Department of Animal Science & Department of Fisheries and Wildlife Michigan State University 1205-I Anthony Hall East Lansing, MI 48824 USA Phone: 1-517-353-5102 E-mail: steibelj at msu.edu

ADD REPLY • link 15.9 years ago Juan Pedro Steibel ▴ 130

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