[BioC] processCGH with snapCGH

[jhs1jjm at leeds.ac.uk]

Quoting Sean Davis <sdavis2 at mail.nih.gov> on Fri 28 Sep 2007 18:20:56
BST:

> jhs1jjm at leeds.ac.uk wrote:
> > 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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> > 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.
>
> Hi, John.
>
> Try:
>
> colnames(MA1$genes)[10] <- 'Position'
>
> Then rerun processCGH.
>
> Sean
>
Hi Sean,

I did the following:

> MA1$genes$Position <- MA1$genes$Start

i.e what you said I think and it worked. Was it just a problem with the
function or have I missed a step somewhere?

Thanks....again!