On 07/29/2014 04:16 AM, carol white wrote: > For a positive quantity like variance, absolute value is not relevant. How about > if a t-test value is used which could be positive or negative? the largest > t-test value in absolute value corresponds to the lowest t-test p-val. Is the > largest t-test value in absolue value taken by findLargest and does it > correspond to the largest variation? findLargest finds the largest value; if you want the largest absolute value then pass abs(<your statistic="" here="">). You can see that findLargest isn't doing anything too fancy > tail(findLargest, 3) 14 tSsp = split.default(testStat, lls) 15 sapply(tSsp, function(x) names(which.max(x))) 16 } > > Many thanks > > > On Tuesday, July 29, 2014 12:30 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > > On 07/28/2014 03:48 AM, carol white wrote: > > Hi, > > Does findLargest find the largest test statistics in absolute value which > > corresponds to the probe with the largest variation? > > Here's an example > > > library(genefilter); library(Biobase) > > data(sample.ExpressionSet) > > eset = sample.ExpressionSet > > x = findLargest(featureNames(eset), rowVars(exprs(eset)), annotation(eset)) > > the first argument is a character vector of feature (probeset) names. The second > argument is the variance of the probeset across all samples. > > The result is > > head(x) > 10002 100128124 100129271 10018 100287387 100505879 > "31667_r_at" "31663_at" "31326_at" "31611_s_at" "31657_at" "31648_at" > > which indicates that for Entrez gene 10002 the probeset with largest variance is > 31667_r_at, etc. > > This could be used to subset the eset > > > eset[x,] > > if you were interested in retaining just the probes with largest variance. > > If the statistic rowVars(exprs(eset)) were replaced with something else (e.g., > interquartile range), then findLargest would of course not return the probe with > largest variance, but with the largest whatever that statistic was. > > Martin > > > > > > > Thanks > > > > carol > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793