Entering edit mode
Daniel Brewer
★
1.9k
@daniel-brewer-1791
Last seen 10.3 years ago
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
P.S,
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] AgiMicroRna_1.0.0 preprocessCore_1.8.0 affy_1.24.0
[4] limma_3.2.1 Biobase_2.6.0
loaded via a namespace (and not attached):
[1] affyio_1.14.0 tools_2.10.1
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
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