[BioC] Problem using justGCRMA

[James W. MacDonald]

Hi Antonio,

On 5/5/2011 4:57 AM, Antonio Mendes wrote:
> Hi
> I'm trying to use justgcrma to normalize data from affy Plasmodium/anopheles
> genome array and am getting the error copied bellow. I'm running version
> 2.13.0 of R and version 2.8.1 of gcrma. Can anybody help how to overcome
> this?
>
> thanks
> Antonio
>
>
>> library(gcrma)
> Loading required package: affy
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation("pkgname")'.
>
>> setwd("H:\\MozzyData")
>> normalized<-justGCRMA()
> Computing affinitiesLoading required package: AnnotationDbi
> [1] "Checking to see if your internet connection works..."
> trying URL '
> http://bioconductor.org/packages/2.8/data/annotation/bin/windows/contrib/2.13/plasmodiumanophelesprobe_2.8.0.zip
> '
> Content type 'application/zip' length 3553447 bytes (3.4 Mb)
> opened URL
> downloaded 3.4 Mb
>
> package 'plasmodiumanophelesprobe' successfully unpacked and MD5 sums
> checked
>
> The downloaded packages are in
>          C:\Users\Antonio\AppData\Local\Temp\RtmpiYHe0U\downloaded_packages
> Loading required package: AnnotationDbi
> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>    there is no package called 'DBI'
> Error: package 'AnnotationDbi' could not be loaded

Looks like you don't have DBI installed. How did you install 
AnnotationDbi? You should always remember to give us the output of 
sessionInfo() so we can see if you have mismatched packages.

The easiest fix will be

source("http://www.bioconductor.org/biocLite.R")
biocLite("AnnotationDbi")

which will ensure you have the correct version, and will install 
dependencies as well. If you want to be doubly sure, you can pass a 
character vector of c("AnnotationDbi","DBI") to biocLite().

Best,

Jim
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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