[BioC] processCGH with snapCGH

[jhs1jjm at leeds.ac.uk]

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="ProbeName")
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