[BioC] cateGOry error

[James W. MacDonald]

Oleg Sklyar wrote:
>>Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it
>>looks like these valus should be GO IDs (element of the categ argument
>>to cateGOry).  Are you sure those values are not in go$go?
> 
> I did the grep and at least the 0024 does not appear there at all. By 
> using %in% I find only 172. But I have further problems, like the 
> following and starting to suspect that something is wrong with character 
> operations:
> 
>  > class(entrez)
> [1] "character"
>  > entrez[120000:120010]
>   [1] NA NA NA NA NA NA NA NA NA NA NA

Is your entrez vector really that long? Any subsetting operation off the 
end of a vector will return NAs.

Best,

Jim


>  > which(is.na(entrez))
> integer(0)
>  > which(entrez=="NA")
> integer(0)
> 
> How can I get onto those NA's?
> 
> 
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "methods"   "base"
> 
> other attached packages:
>     Category      Matrix     lattice  genefilter    survival    annotate
>      "2.2.1" "0.9975-11"    "0.15-4"    "1.14.1"      "2.31"    "1.14.1"
>           GO        KEGG       graph     Biobase     biomaRt       RCurl
>     "1.16.0"    "1.16.0"    "1.14.0"    "1.14.0"    "1.10.0"     "0.8-0"
>          XML
>      "1.9-0"
> 
> _______________________________________________
> 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
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.