[BioC] incomplete final row of every block

[Jean Yee Hwa Yang]

Hi Mark,

If you were trying out median normalization, try
maNorm(my.oe, norm="m")

How many lines do you have in the layout file?  

In order for print-tip loess to work on your array, you will need to set
up my.layout at maSub properly. This should be a logical vector of length
7056.  For the corresponding position of 9 * 16 = 144 empty spots (that
are not in the data file), the value should be set to "FALSE".

Cheers

Jean


As for setting up the layout, I assume the control columns in

> 
> control<-rep(0,dim(layout)[1])
> control[grep("TH",as.character(layout$Gene))]<-1
> maControls(my.layout)<-as.logical(control)
> 
> # read in data
> my.oe<-read.marrayRaw(as.character(my.targets at maInfo$Names),
>                       name.Gf="F532 Location",name.Gb="B532 Location",
>                       name.Rf="F635 Location",name.Rb="B635 Location",
>                       gnames=my.gnames,layout=my.layout,targets=my.targets)
> 
> # median normalize.
> my.norm<-maNormMain(my.oe,f.loc=list(maNormLoess()))