[BioC] kooperberg syntax fix

scholz@Ag.arizona.edu scholz at Ag.arizona.edu
Thu Sep 1 15:32:27 CEST 2005


Mick Watson was nice enough to help me fix a problem I was having using the
kooperberg background correction function and asked me if I wouldn't mind
posting a summary of our discussion so that others may benefit. Thanks to Mick
for the following help.

I was receiving an error message when I tried to run the kooperberg function on
my genepix-generated dataset. Despite having gal files that seemed to work with
other functions, I would receive one of the following error messages: 

"Error in getLayout(get(genepixFiles[1])) : gal needs to have columns Block, Row
and Column"


"Error in "[.data.frame"(slide, , "F635.Mean") :undefined columns selected"

After sending Mick my gal and gpr files, he was able to figure out that my
problems were:

1. The example kooperberg script provided under ?kooperberg, which I was using
as a template for my own function, has its skip argument set to 26, whereas the
data in my gal file started on line 31.

2. I had # characters in my annotation column (e.g. tubulin #6), which R
translated as a comment to be ignored.

Mick sent the following fix:

genepixFiles <- dir(pattern="*\\.gpr$")
read.series(genepixFiles, suffix=NULL, skip=31, sep="\t",
comment.char="", quote="\"")
layout <- getLayout(get(genepixFiles[1]))
RGmodel <- kooperberg(genepixFiles, layout=layout)
gal <- readGAL("MOB-1-3.anno.gal")
RGmodel$genes <- gal 

the skip and comment.char arguments address these two issues. Thanks Mick!


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