[BioC] processCGH with snapCGH

[Sean Davis]

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
>>
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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.

Hi, John.

Try:

colnames(MA1$genes)[10] <- 'Position'

Then rerun processCGH.

Sean