[BioC] genefilter displaying the expression set

[James MacDonald]

Hi Dharrini,

filtered.tumor <- tumor[ans,]

Should give you what you want.

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
>>> dhaarini s <dhaarini87 at gmail.com> 02/25/09 3:43 AM >>>
Hi all!
I am new to R and Bioconductor. I am having a dataset of 22283 genes and 190
samples. Due to the huge size of the data, I want to filter some irrelevant
genes. I tried the "genefilter" package of BioC, but then understand that it
does gene filtering by simply displaying whether the gene satifies the
filter condition or not by marking it as TRUE. This is how I proceeded:
> library(genefilter)
> f1 <- kOverA(5, 10)
> flist <- filterfun(f1)
> ans <- genefilter(tumor, flist)
(The object "tumor" contains my expression dataset.) The output is something
like this:
"x"
"1007_s_at" TRUE
"1053_at" FALSE
"117_at" FALSE
"121_at" FALSE
"200001_at" TRUE
"200002_at" TRUE
..........................
But, Iwould like to know whether the genefilter will return me an expression
set containing the filtered genes and their expression values for the
samples. Please help me out!
Thanks in advance.
Regards,
Dhaarini

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