Entering edit mode
jhs1jjm@leeds.ac.uk
▴
230
@jhs1jjmleedsacuk-2338
Last seen 10.3 years ago
Hi all,
Despite searching the archives, i'm still having problems with the
processCGH
function. I've done the following:
> #read intensities
> RG1Pro <- read.maimages(targets$File_names,
source="agilent",columns=list(R="rProcessedSignal",G="gProcessedSignal
"))
> #read positional info about clones
> RG2 <- readPositionalInfo(RG1Pro,source="agilent")
> #specify reference channel
> RG2$design <- c(-1,-1)
> #create logratio(data already background adjusted and dye bias
normalized)
> MA1 <- MA.RG(RG2)
> #tidy MAList object
> MA2 <- processCGH(MA1,maxChromThreshold=24,minChromThreshold=1,ID="P
robeName")
Error in order(na.last, decreasing, ...) :
argument 2 is not a vector
I didn't think argument 2 was meant to be a vector
Using default values gives me the same result:
> MA2 <- processCGH(MA1,ID="ProbeName")
Error in order(na.last, decreasing, ...) :
argument 2 is not a vector
My MA1$genes seems to be set up ok:
> colnames(MA1$genes)
[1] "Row" "Col" "ProbeUID" "ControlType"
[5] "ProbeName" "GeneName" "SystematicName" "Description"
[9] "Chr" "Start" "End"
Might it be something to do with probes with no location information
I used the following to remove probes with no location info:
> MA1$genes <- MA1$genes[!is.na(MA1$genes$Chr)) & MA1$genes$Chr !=
"",]
Usage:
processCGH(input, maxChromThreshold = 22, minChromThreshold
= 1, method.of.averaging = NULL, ID = "ID",
prop.missing = 0.1)
Any input is much appreciated
John
