[R] problem with merge

[Mark W Kimpel]

I have used merge regularly and thought I understood how it worked, but 
I must not. I have two dataframes with identical colnames from two 
different experiments, TL01 and LC01. Each dataframe has a column named 
"Entrez.Gene", which I have converted to "as.character" just to make 
sure merge is not looking at factor levels. Because I have done some 
filtering, the Entrez.Gene values in each experiment overlap but are not 
identical. I want to produce a summary report with only those 
identifiers found in each experiment. I could do this with intersect and 
matching, but I thought merge could easily do this.

Below is my code and sessionInfo. For some reason there are over twice 
as many rows as I would expect. I can't quite figure out which arguments 
I have screwed up. What am I missing? It has to be something simple, I'm 
just not seeing it.  Thanks, Mark

 > TL01.LC01.data <- merge(TL01.data, LC01.data, by = "Entrez.Gene", 
all.x = FALSE, all.y = FALSE, suffixes = c(".TL01",".LC01"))
 > length(intersect(TL01.data$Entrez.Gene, LC01.data$Entrez.Gene))
[1] 13401
 > dim(TL01.LC01.data)
[1] 29471    57
 > dim(TL01.data)
[1] 16479    29
 > dim(LC01.data)
[1] 16479    29
-- 
 > sessionInfo()
R version 2.7.0 Under development (unstable) (2008-03-05 r44683)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
  [1] affycoretools_1.11.4 annaffy_1.11.5       KEGG.db_2.1.3
  [4] gcrma_2.11.4         matchprobes_1.11.1   biomaRt_1.13.9
  [7] RCurl_0.8-3          GOstats_2.5.2        Category_2.5.7
[10] genefilter_1.17.12   survival_2.34        RBGL_1.15.7
[13] annotate_1.17.11     xtable_1.5-2         GO.db_2.1.3
[16] AnnotationDbi_1.1.26 RSQLite_0.6-8        DBI_0.2-4
[19] graph_1.17.17        limma_2.13.6         affy_1.17.9
[22] preprocessCore_1.1.5 affyio_1.7.15        Biobase_1.99.2

loaded via a namespace (and not attached):
[1] cluster_1.11.10 XML_1.93-2

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
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mwkimpel<at>gmail<dot>com