[BioC] re incomplete analysis in Deseq
Steve Lianoglou
mailinglist.honeypot at gmail.com
Tue Mar 6 22:21:26 CET 2012
Hi,
On Tue, Mar 6, 2012 at 3:28 PM, Wolfgang Huber <whuber at embl.de> wrote:
>
> Hi Julian, Kasper
>
> in this case you will need to (and as I am sure, be able to) come up with
> another method for estimating size factors that works on these data. Why not
> try with the 'colSums'?
Couldn't we just-as-well adapt the estimateSizesFactorsForMatrix
function to step over the (row,col) bins that have the 0 counts
instead of skipping over rows that only have 1 0 element?
Something like so:
#########
esfm <- function(counts, locfunc=median) {
## Can't use info from rows that are all 0, so axe them
counts <- counts[rowSums(counts) > 0,]
logc <- log(counts)
loggeomeans <- apply(logc, 1, function(x) {
use <- is.finite(x)
sum(x[use]) / sum(use)
})
apply(logc, 2, function(lc) {
use <- is.finite(lc)
exp(locfunc(lc[use] - loggeomeans[use]))
})
}
##########
¿mas o menos?
-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
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