[BioC] matrix row/column displayed as a list

[Sean Davis]

On Tuesday 10 April 2007 05:15, Daniel Brewer wrote:
> Seth Falcon wrote:
> > Sean Davis <sdavis2 at mail.nih.gov> writes:
> >> 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_IDENTIFI
> >>>CATIO 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.
> >
> > This is very strange.  Daniel, can you post the matrixExample.rdata
> > file somewhere I could download it?
> >
> > + seth
>
> Hi,
> Here is a URL where you can download the file from:
> http://www.crukdmf.icr.ac.uk/matrixExample.rdata
>
> Also, to give a bit of background.  This matrix is a cut down version of
> a matrix I constructed from a GSE object using the GEOquery package.

Dan,

I see the same thing you see (sessionInfo() below).  I have no idea why this 
is the way it is (any ideas, Seth?), but to fix the problem, it looks like 
you can simply do something like:

newMatrix <- matrix(matrixExample2,ncol=ncol(matrixExample2))

sessionInfo():
R version 2.5.0 alpha (2007-03-26 r40902)
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] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"


Sean