[BioC] matrix row/column displayed as a list

[Seth Falcon]

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_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.  

This is very strange.  Daniel, can you post the matrixExample.rdata
file somewhere I could download it?

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org