Hi,

I have a question regarding the Illumina Human Methylation 450k array and the genefilter package.
I used the 'nsfilter' function in gene filter to remove probes that have low variance across samples. When I checked the documentation for nsfilter, I found out that applying the function removes 50% of the probes by default. 

I computed the variance for each probe in the remaining probes and for the removed probes separately. When I plot the density for each set of variances, they overlap completely showing that both sets have most of their probes with variance close to zero and few with high variance.

This leaves me wondering how nsfilter actually filters probes, as it doesn't appear from the plot that the probes with the lowest variances are removed. 

What would be the best way to filter out low variance probes in 450k data? If the default value in nsfilter is set to 50% assuming that 40% of genes in a cell are not expressed, what percentage cutoff can be used for methylation data?
Would be great if anyone can explain it.

Thanks,
Khadeeja

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