[BioC] problem with justRMA in 2.10.0

[James W. MacDonald]

Hi Joseph,

Joseph Dougherty wrote:
> Hello,
> 
> Has this bug been resolved?  I am working in R 2.10 for the first time (also
> a on a new linux server) and I am getting a strange error with ReadAffy().
> I don't have this error on my Windows machine, or our old server, which are
> still on earlier versions of R.

The bug in justRMA() didn't affect ReadAffy().

>> dat<-ReadAffy()
> Error in value[[3L]](cond) :
>   row names supplied are of the wrong length
>   AnnotatedDataFrame 'initialize' could not update varMetadata:
>   perhaps pData and varMetadata are inconsistent?
> 
> I am just trying to load all of the Cel files in a directory.  I get the
> same message without a phenoData file (the way I usually run it), or if I
> make a simple one, which suggests to me this error message is probably not
> germane.     This could also be some other problem with the new server or
> the R install, but since Frasier had a similar error message, I thought I
> would check with you all first, before trying to make guess on what else
> could be going on.  I first got the error on Thursday.  I deleted and
> re-installed by bioconductor libraries tonight and stil get the error.

You always need to supply us with your sessionInfo(). I get this to work 
with a new version of R, so it is likely you have mis-matched packages.

 > dat <- ReadAffy()
 > sessionInfo()
R version 2.10.0 Patched (2009-11-05 r50317)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] affy_1.24.1   Biobase_2.6.0

loaded via a namespace (and not attached):
[1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0

Best,

Jim


> 
> Thanks,
> 
> Joe Dougherty
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> 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

-- 
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