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
>
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