[BioC] Removing bad flag spot using marray

[Julien Bauer]

Hi,
I just getting started with bioconductor, so my question might be easy to
answer...
I have a problem with the read.marrayRaw method. We are not using genepix
anymore, we use a new software call BlueFuse .
It allow us to save a lot of time as it got a really good method to find the
spot and automatically remove the background. It create two new "clean" tif
files as well. My problem come after inputting data using marrayLayout , if
I take all the data in and then create a marrayRaw I can't find a way to
remove afterwards the bad flagged spots or the negative control or the empty
spots (which have specific id for the controls or a tag "yes" or "no" for
bad flagged (yes means bad flagged).  If I removed them before inputting the
data I get a error when using read.marrayRaw:
Error in "[<-"(`*tmp*`, , f, value = as.matrix(dat[, name.Gf])) :
        number of items to replace is not a multiple of replacement length
I guess it have something to do with the layout and some missing values in
block, column...
Any idea?
Thanks,

--------------------------------------------
Julien Bauer, Bioinformatics Research Assistant
Micro Array Group
Department of Pathology
University of Cambridge, Tennis Court Road
Cambridge CB2 1QP UK
mailto: jb393 at cam.ac.uk