[BioC] matrix row/column displayed as a list

[Sean Davis]

On Tuesday 03 April 2007 06:04, Daniel Brewer wrote:
> Sean Davis wrote:
> > On Monday 02 April 2007 12:43, Daniel Brewer wrote:
> >> Sorry it has taken so long for me to reply, I have been away.  I enclose
> >> a cut down version of my expression matrix.  Here is an example of my
> >>
> >> session:
> >>> matrixExample2
> >>
> >>               GSM89679 GSM89681 GSM89683 GSM89684 GSM89685
> >> IMAGE:1031489 -0.828   -0.618   -1.154   -0.975   -0.59
> >> IMAGE:1031497 -0.426   -0.515   -0.765   -0.443   -0.713
> >> IMAGE:1031509 -0.301   -0.923   1.437    -0.836   0.461
> >> IMAGE:1031510 -0.976   -0.814   0.268    -1.331   0.913
> >> IMAGE:1031516 -2.066   0.134    0.332    -2.018   1.489
> >> IMAGE:1031532 -0.754   -2.202   -1.438   -2.054   -0.836
> >
> > Hi, Dan.
> >
> > What does:
> >
> > class(matrixExample2) show?
> >
> > What happens if you do:
> >
> > matrixExample3 <- as.matrix(matrixExample2)
> > class(matrixExample3)
> > matrixExample3[,1]
> > class(matrixExample3[,1])
> >
> > Finally, what is the output of sessionInfo()?
> >
> > Sean
>
> Hi Sean,
>
> Here are the results of the commands you suggested.
>
> > load("matrixExample.rdata")
> > class(matrixExample2)
>
> [1] "matrix"
>
> > matrixExample3 <- as.matrix(matrixExample2)
> > class(matrixExample3)
>
> [1] "matrix"
>
> > matrixExample3[,1]
>
> $`IMAGE:1031489`
> [1] -0.828
>
> $`IMAGE:1031497`
> [1] -0.426
>
> $`IMAGE:1031509`
> [1] -0.301
>
> $`IMAGE:1031510`
> [1] -0.976
>
> $`IMAGE:1031516`
> [1] -2.066
>
> $`IMAGE:1031532`
> [1] -0.754
>
> > class(matrixExample3[,1])
>
> [1] "list"
>
> > sessionInfo()
>
> R version 2.4.1 (2006-12-18)
> 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_NA
>ME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATIO
>N=C
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
> [7] "base"
>
> So that does not provide much insight. Have you got any other suggestions?

Well, you've got me stumped, but that isn't too hard to do.  

Sean