Question: genefilter
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gravatar for carol white
5.4 years ago by
carol white680
European Union
carol white680 wrote:
Hi, Does findLargest find the largest test statistics in absolute value which corresponds to the probe with the largest variation? Thanks carol [[alternative HTML version deleted]]
probe • 583 views
ADD COMMENTlink modified 5.4 years ago by Martin Morgan ♦♦ 24k • written 5.4 years ago by carol white680
Answer: genefilter
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gravatar for Martin Morgan
5.4 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k 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 > 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
ADD COMMENTlink written 5.4 years ago by Martin Morgan ♦♦ 24k
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? Many thanks On Tuesday, July 29, 2014 12:30 PM, Martin Morgan <mtmorgan@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@r-project.org > 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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.4 years ago by carol white680
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
ADD REPLYlink written 5.4 years ago by Martin Morgan ♦♦ 24k
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