[BioC] calculating median expression between to identical gene names in data frame
ramasamy at cancer.org.uk
Sat Mar 15 03:41:54 CET 2008
I am assuming that you want to "average" the gene profiles.
See if this works:
colMedians <- function(mat) apply(mat, 2, median)
sapply( split( df, gids ), colMedians )
This is computationally inefficient as the number of rows increase but
this should be reasonably fast for 180 rows.
Srinivas Iyyer wrote:
> Dear group,
> I have a data frame with 180 rows and 25 coloumns
> (data from a affy experiment). I have 10 normals and
> 15 cancer lines.
> of 180 I have some duplicate gene names (arising from
> two different probesets for a single gene).
> I want to calculate the median expression value for
> these two identical genes.
> here I have 6 samples and 2 genes.
> gids N1 N2 N3 T1 T2 T3 T4
> G1 10 12 11 40 46 39 46
> G1 8 10 8 35 46 32 53
> could any one please help me How can I calculate the
> median expression for these two identical genes.
> After I do this, I want to do clustering.
> thank you.
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