[BioC] matrix row/column displayed as a list

[Daniel Brewer]

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_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
> 


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.

Many thanks for looking into this.

Dan

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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