[BioC] incomplete final row of every block

[Mark Robinson]

Hi.

We have these homemade arrays that have nothing printed in the last 9 columns 
of the last row of each grid.  4x4 grids, 21x21 spots in each grid == 7056 
possible of which we have only 6912 and 9*16 as empty.  So, the data files have 
6913 lines (one for header).

I'm new to Bioconductor and am having trouble getting it to do a Loess 
normalization.  Here is what I have:

# make gene lists, sample lists
my.targets<-read.marrayInfo("mySamples.txt")
my.gnames<-read.marrayInfo("layout.txt",info.id=2,label=2,skip=1)

# make layout
layout<-read.table("layout.txt",sep="\t",header=T)
my.layout<-read.marrayLayout(ngr=4,ngc=4,nsr=21,nsc=21)
maSub(my.layout)<-layout$Control!="control"

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()))

--This last line gets the following error:
> my.norm<-maNormMain(my.oe,f.loc=list(maNormLoess()))
Error: dim<- : dims [product 6307] do not match the length of object [6439]
In addition: Warning message: 
longer object length
        is not a multiple of shorter object length in: samplesub & which & 
subset & good 


--Also, I get an error from the following:
maGeneTable(my.oe)
> maGeneTable(my.oe)
Error in data.frame(GR = maGridRow(object), GC = maGridCol(object), SR = 
maSpotRow(object),  : 
        arguments imply differing number of rows: 6439, 6912

I'm not surprised by the errors, I'm just not exactly sure how to input the 
data in the correct way ... well, without adding dummy lines into my data file 
and layout file.  Is there an easier way?

layout.txt looks like:
...
92	YDL107W	1	5	8	probe
93	YDL109C	1	5	9	probe
94	YDL199C	1	5	10	probe
...



Thanks,
Mark





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