Re: [R] problem with merge

From: Don MacQueen <macq_at_llnl.gov>
Date: Tue, 18 Mar 2008 08:16:09 -0700

Do any of your Entrez.Gene values appear in more than one row in either of the dataframes?

For example:

> dfa <- data.frame( a = c('A','A','B','C') , x= 1:4)
> dfb <- data.frame( a = c('A','B','B','D'), y=1:4)
>
> merge(dfa,dfb)

   a x y
1 A 1 1
2 A 2 1
3 B 3 2
4 B 3 3

> length(intersect(dfa$a, dfb$a))

[1] 2

-Don

At 8:40 PM -0400 3/17/08, Mark W Kimpel wrote:
>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
>(317) 204-4202 Home (no voice mail please)
>
>mwkimpel<at>gmail<dot>com
>
>______________________________________________
>R-help_at_r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062

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Received on Tue 18 Mar 2008 - 15:29:59 GMT

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