[BioC] filter low expression tags

[Steve Lianoglou]

Hi,

On Wed, Nov 28, 2012 at 10:14 PM, Vittoria Roncalli <roncalli at hawaii.edu> wrote:
> Hi,
>
> I would like to understand how the filter of low expression tags works. If
> I run the command
>
>>keep <- rowSums (cpm(d)>100) >=2
> d <- d[keep,]
> dim(d)
>
> as in the use guide page 32, this means that I am using a cutoff of 100cpm,
> but how are treated the 2 samples? Did are they averaged and then the low
> tags are removed?
> Is each sample considered separate and filtered by itself?
> Thanks foe the help in advance

How many samples (columns) do you have?

You should first look at the output of `cpm(d) > 100` to see what you
are getting -- this will be a logical (boolean) matrix that has the
same dimensionality as `cpm(d)`.

rowSums( a logical matrix )

returns a vector that is as long as there are rows in the logical
matrix, and each value indicates how many columns are TRUE in that
row.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact