Dear Sherosha, If you use topTable(fit, coef=c(1,2,3), lfc=1) then the genes with be ranked by F-statistic, and any probe satisfying lfc for any one contrast will be considered. Regarding decideTests() and method="separate", it doesn't make sense to me to use a multiple-contrast cutoff unless you also use a multi-contrast test statistic. Best wishes Gordon > Date: Fri, 23 Jan 2009 17:40:07 -0500 > From: Sherosha Raj <sherosha at="" gmail.com=""> > Subject: Re: [BioC] Help: LIMMA-decideTests and lfc option > To: James MacDonald <jmacdon at="" med.umich.edu="">, > bioconductor at stat.math.ethz.ch > Message-ID: > <6cdc8dd00901231440w44b651f4l720d6af746771dfb at mail.gmail.com> > Content-Type: text/plain > > Hi Jim > Thank you for the clarification. Is it possible to have a conditional > selection based on the lfc in decideTests? > Eg. if I had three contrasts and there is a probeset with lfc that satisfies > my cutoffs in just ONE contrast but not in the others, and I would still > like it to be considered? > > > Thank you again. > Regards, > Sherosha > > > 2009/1/23 James MacDonald <jmacdon at="" med.umich.edu=""> > >> Hi Sherosha, >> >> The lfc argument applies to all the contrasts you have made individually. >> So for instance if you have three contrasts and for one probeset they were >> (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would >> pass that filter and the second would not. >> >> Best, >> >> Jim >> >> James W. MacDonald, M.S. >> Biostatistician >> Hildebrandt Lab >> 8220D MSRB III >> 1150 W. Medical Center Drive >> Ann Arbor MI 48109-0646 >> 734-936-8662 >>>>> Sherosha Raj <sherosha at="" gmail.com=""> 01/22/09 2:28 PM >>> >> Hello everyone >> >> I am unsure how to interpret the lfc option in the multiple testing >> algorithm decideTests: >> decideTests(object,method="separate",adjust.method="BH",p.value=0.0 5,lfc=0) >> >> The explanation given is: >> "If lfc>0 then contrasts are judged significant only when the >> log2-fold change is at least this large in absolute value. For >> example, one might choose lfc=log2(1.5) to restrict to 50% changes or >> lfc=1 for 2-fold changes. In this case, contrasts must satisfy both >> the p-value and the fold-change cutoff to be judged significant." >> >> What is meant exactly? Is it within a particular contrast that the >> log2FC>0 for a particular probeset? Or is it comparing across all the >> contrasts specified? >> >> If some one could offer a clarification I would be most grateful. >> Thank you. >> >> -- >> Regards, >> Sherosha

I will use topTable in this case to pick probesets by fold change. Thank you for the hint Gordon. -- Regards, Sherosha 2009/1/25 Gordon K Smyth <smyth@wehi.edu.au> > Dear Sherosha, > > If you use > > topTable(fit, coef=c(1,2,3), lfc=1) > > then the genes with be ranked by F-statistic, and any probe satisfying lfc > for any one contrast will be considered. > > Regarding decideTests() and method="separate", it doesn't make sense to me > to use a multiple-contrast cutoff unless you also use a multi- contrast test > statistic. > > Best wishes > Gordon > > > Date: Fri, 23 Jan 2009 17:40:07 -0500 >> From: Sherosha Raj <sherosha@gmail.com> >> Subject: Re: [BioC] Help: LIMMA-decideTests and lfc option >> To: James MacDonald <jmacdon@med.umich.edu>, >> bioconductor@stat.math.ethz.ch >> Message-ID: >> <6cdc8dd00901231440w44b651f4l720d6af746771dfb@mail.gmail.com> >> Content-Type: text/plain >> >> Hi Jim >> Thank you for the clarification. Is it possible to have a conditional >> selection based on the lfc in decideTests? >> Eg. if I had three contrasts and there is a probeset with lfc that >> satisfies >> my cutoffs in just ONE contrast but not in the others, and I would still >> like it to be considered? >> >> >> Thank you again. >> Regards, >> Sherosha >> >> >> 2009/1/23 James MacDonald <jmacdon@med.umich.edu> >> >> Hi Sherosha, >>> >>> The lfc argument applies to all the contrasts you have made individually. >>> So for instance if you have three contrasts and for one probeset they >>> were >>> (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would >>> pass that filter and the second would not. >>> >>> Best, >>> >>> Jim >>> >>> James W. MacDonald, M.S. >>> Biostatistician >>> Hildebrandt Lab >>> 8220D MSRB III >>> 1150 W. Medical Center Drive >>> Ann Arbor MI 48109-0646 >>> 734-936-8662 >>> >>>> Sherosha Raj <sherosha@gmail.com> 01/22/09 2:28 PM >>> >>>>>> >>>>> Hello everyone >>> >>> I am unsure how to interpret the lfc option in the multiple testing >>> algorithm decideTests: >>> >>> decideTests(object,method="separate",adjust.method="BH",p.value=0. 05,lfc=0) >>> >>> The explanation given is: >>> "If lfc>0 then contrasts are judged significant only when the >>> log2-fold change is at least this large in absolute value. For >>> example, one might choose lfc=log2(1.5) to restrict to 50% changes or >>> lfc=1 for 2-fold changes. In this case, contrasts must satisfy both >>> the p-value and the fold-change cutoff to be judged significant." >>> >>> What is meant exactly? Is it within a particular contrast that the >>> log2FC>0 for a particular probeset? Or is it comparing across all the >>> contrasts specified? >>> >>> If some one could offer a clarification I would be most grateful. >>> Thank you. >>> >>> -- >>> Regards, >>> Sherosha >>> >> [[alternative HTML version deleted]]