[BioC] Removing bad flag spot using marray

Julien Bauer jb393 at cam.ac.uk
Thu Jul 1 18:01:05 CEST 2004

I just getting started with bioconductor, so my question might be easy to
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?

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

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