[BioC] probe information from cel image

[Laurent Gautier]

It is possible (and hopefully not too complicated to use).
To get info about what is at x=100, y=50 you can do:

If you have the .CDF file around:

cdf <- read.cdffile("corresponding_cdf.cdf")
cdf at name.levels[cdf at name[100, 50]]

If you do not have it, one strategy is to get close to what
is above:

m.name <- matrix(as.integer(NA), nr=abatch at nrow, nc=abatch at ncol)
g.i <- indexProbes(abatch, which="both")

for (i in seq(along=g.i)) {
  xy <- indices2xy(g.i[[i]], abatch=abatch)
  m.name[xy] <- i
}

m.name.levels <- names(g.i)

m.name.levels[m.name[100, 50]]



For interactivity, you can implement easily something using the
R function 'locator'.


I am working on a more general scheme to shuttle from indices to info(*),
and to positions to info... but I am not sure how fast this will come
true...


L.


(*: not only probe set id, but anything else one would fashion...)
On Wed, Jun 25, 2003 at 01:12:57PM +1000, Matthew Hobbs wrote:
> In affy the plotLocation function allows me to display probe locations on a 
> celfile image, but is it possible to go in the other direction i.e. derive 
> the identities of probes related to a particular area on an image (perhaps 
> specified interactively by pointing and clicking).
> 
> Thanks
> 
> -- 
> ----------------------------------------------------------------------
> Matthew Hobbs
> 
> Garvan Institute of Medical Research
> 384 Victoria St            Ph   : (02) 9295 8327
> Darlinghurst                
> http://www.garvan.org.au        email:  m.hobbs at garvan.org.au
> 
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