At 07:12 PM 1/2/2006, Naomi Altman wrote: >I would like TopTable to print: > >p-value >adjusted "p-value" > >using whatever set of p-values is relevant - i.e. either the t-test >for a coefficient or the F-test for a set of coefficients or the >overall F-test. I concur... it would be helpful to see whether or not p-value adjustment had been done in the object created by topTable, rather than having to look back to the code when topTable was called (if it's still around...). Furthermore, it is possible to indicate which adjustment has been done by the name of the column, e.g. BH.p or BY.p? I understand these requests may not be feasible if the resulting object needs to have the same number of columns with the same names every time. A couple of other suggestions for minor improvements on topTable functionality: 1) have "ID" be an option for resort.by; 2) have "all" be an option (or even the default!) for number. This second request is really me just being lazy and not wanting to look up and type in the number of genes, or coding it by out.table <- topTable(fit, number=length(fit$genes[,1])) Happy New Year! Jenny >--Naomi > >At 08:00 PM 1/2/2006, Gordon Smyth wrote: > >topTable() doesn't have a facility for sorting on or presenting the > >F-statistics, because it is individual coefficient orientated. > > > >I have toyed with the idea that perhaps topTable() should output a > >table based on the F-statistic when the argument 'coefficient' is > >set to NULL. In other words topTable() would give individual coef > >significance when a coef is specified, otherwise it would give > >overall significance. Would you find that a useful facility? > > > >Best wishes > >Gordon > > > >At 09:04 AM 3/01/2006, Naomi Altman wrote: > >>I did not get the original posting, but doesn't Sohail just need > >>"TopTable" for this? > >> > >>--Naomi > >> > >>At 08:51 AM 1/2/2006, Gordon Smyth wrote: > >>>Dear Sohail, > >>> > >>>Well, there are lots of ways to generate such a table. Perhaps the > >>>simplest is > >>> > >>> fitsel <- fit2[sel.dif, ] > >>> as.data.frame( fitsel ) > >>> > >>>Best wishes > >>>Gordon > >>> > >>> >Date: Tue, 20 Dec 2005 14:03:43 -0500 > >>> >From: "Khan, Sohail" <khan at="" cshl.edu=""> > >>> >Subject: [BioC] Time course experiment.... > >>> >To: <bioconductor at="" stat.math.ethz.ch=""> > >>> > > >>> >Dear List, > >>> > > >>> >I have performed a time course analysis using limma, as described in > >>> >"Bioinformatics and Computational Biology Solutions ........". > >>> >How can I get a list of differentially expressed genes? I've tried > >>> >the code below: > >>> >sel.dif<-p.adjust(fit2$F.p.vlaue,method="fdr") <0.05 > >>> >This produces a logical vector, right?. I would like a table of > >>> >differentially expressed genes with p vales etc. Sorry, if I missed > >>> >this in the limma user's guide. Thanks for any suggestions. > >>> > > >>> > > >>> >Sohail Khan > >>> >Scientific Programmer > >>> >COLD SPRING HARBOR LABORATORY > >>> >Genome Research Center > >>> >500 Sunnyside Boulevard > >>> >Woodbury, NY 11797 > >>> >(516)422-4076 > >>> > >>>_______________________________________________ > >>>Bioconductor mailing list > >>>Bioconductor at stat.math.ethz.ch > >>>https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >>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 > > > >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

On Tue, January 3, 2006 11:24 pm, Sean Davis wrote: > On 1/2/06 8:00 PM, "Gordon Smyth" <smyth at="" wehi.edu.au=""> wrote: >> topTable() doesn't have a facility for sorting on or presenting the >> F-statistics, because it is individual coefficient orientated. >> >> I have toyed with the idea that perhaps topTable() should output a >> table based on the F-statistic when the argument 'coefficient' is set >> to NULL. In other words topTable() would give individual coef >> significance when a coef is specified, otherwise it would give >> overall significance. Would you find that a useful facility? > > Gordon, > > I do think your suggested additions would be useful. In addition, I often > find myself generating a large spreadsheet based on the output of a number > of individual coefficients so that the biologist can use that spreadsheet in > something like Excel to sort and filter data at will. > > While less statistically palatable than the current method and your F-stat > extension, would it be possible to include a third variation such that the > coefficient argument could be set to a vector? This then leaves the > question of how to "rank" or "sort" genes, but one could choose arbitrarily > to order by the input to topTable (the order of the fit object--I typically > use ALL genes for output) or to use the first value in the coefficient > vector as the "key" coefficient. For complicated experiments, I think many > biologists like to see how a gene looks for multiple coefficients > simultaneously. > > Thanks, > Sean Hi Sean, I'm not sure what output you are thinking of for vector coef. How is it different from write.fit(fit) or write.fit(fit[,selectedcoefs]) ? In general, the use of contrasts is intended for looking at subsets of coefficients. E.g., contrasts.fit() followed by topTable() with coef=NULL could rank genes on the F-statistic for any selection of coefficients or contrasts. My thought of what a vector coef argument to topTable() would be is that it should (i) compute the fit object for the set of contrasts defined by those coefficients and (ii) output a top-table ranked by the F-statistics for that set of contrasts. Cheers Gordon