[BioC] processCGH with snapCGH

[jhs1jjm at leeds.ac.uk]

Quoting jhs1jjm at leeds.ac.uk on Fri 28 Sep 2007 17:12:54 BST:

> 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
>
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>

Additionally part of the code for the processCGH function orders the Chr
as follows:

ord <- order(MA$genes$Chr, MA$genes$Position)
I'm not sure where the variable MA$genes$Postion has come from as
readPositionalInfo didn't create it.

John