[BioC] cvArray error from AgiMicroRna package

[Daniel Brewer]

On 11/02/2010 4:18 PM, Daniel Brewer wrote:
> Hello,
> 
> I am trying to analyse a series of Agilent microRNA arrays using the
> AgiMicroRna package.  When I run the cvArray function I get the
> following error:
> Error in cvArray(dd.micro, "MeanSignal", targets.micro, verbose = TRUE) :
>   NOT DUPLICATED ProbeName in chip
> 
> Any ideas what this means and how to fix it?
> 
> Interetsing dd.micro$genes does not have a column called ProbeName or
> GeneName like it suggests in the Vignette, but it does have ProbeUID.
> This is a bit odd as the datafiles do have a column called ProbeName and
> GeneName.
> 
> The steps I have taken before this are as follows:
>> library("AgiMicroRna")
>> targets.micro <- readTargets(infile="Input/Targets.csv",verbose=TRUE)
> #TotalProbeSignal
>> td <- getwd()
>> setwd("Input/FE files")
>> dd.micro <- readMicroRnaAFE(targets.micro,verbose=TRUE)
>> setwd(td)
> 
> Many thanks
> 
> Dan

I fixed this by allowing more columns form the genes column to be
retained by readMicroRnaAFE.

Dan


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