[BioC] Stuck with Yeast Tiling Array

[Richard Harrison]

Thanks Joern,
The first part works great:

 > sampleNames(richard)
[1] "./ucont.CEL" "./utest.CEL"

I now see the above.

I was worried that when i use the davidTiling dataset and i do  
sampleNames, each Cel file is preceeded by a number, so what i would  
expect to see is:

[1] "./ucont.CEL"
[2] "./utest.CEL"

What I actually want to do is normalise the arrays, by using the  
normalize by reference function. I now get the following error:


 >isDNA = richard$nucleicAcid == "ucont"
 > isRNA = richard$nucleicAcid == "utest"
 > pm = PMindex(probeAnno)
 > bg= BGindex(probeAnno)
 > yn = normalizeByReference (richard [,isRNA] , reference = richard  
[,isDNA], pm = pm, background + 	= bg)

Error in normalizeByReference(richard[, isRNA], reference = richard[,  :
         There is nothing to normalize in 'x'.


Any suggestions? Here is my sessionInfo:

 > sessionInfo()
R version 2.5.1 (2007-06-27)
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.U 
TF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF- 
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID 
ENTIFICATION=C

attached base packages:
[1] "splines"   "grid"      "tools"     "stats"     "graphics"   
"grDevices"
[7] "utils"     "datasets"  "methods"   "base"

other attached packages:
davidTiling           GO  tilingArray       pixmap  geneplotter       
lattice
      "1.0.4"     "1.16.0"     "1.14.0"      "0.4-7"     "1.14.0"     
"0.15-11"
     annotate   genefilter     survival          vsn        limma   
strucchange
     "1.14.1"     "1.14.1"       "2.32"      "2.2.0"      
"2.10.5"      "1.3-2"
     sandwich          zoo RColorBrewer         affy        
affyio      Biobase
      "2.0-2"      "1.3-2"      "0.2-3"     "1.14.2"      "1.4.1"      
"1.14.1"


Many thanks,
Richard



On 19 Sep 2007, at 16:58, Joern Toedling wrote:

> Hi Richard,
>
>> cels= dir(pattern=".CEL")
>> richard  = readCel2eSet(cels)
>>
>> this renames my arrays to "1" and "2". How can i rename these to
>> their original names?
>>
>
> you can set the sampleNames of an ExpressionSet object by
> sampleNames(richard) <- ....
> for example:
> sampleNames(richard) <- cels
>
>>> dim(richard)
>> Features  Samples
>> 6553600        2
>>> sampleNames (richard)
>> [1] "1" "2"
>>>
>>
>>
>> Second it puts them in one column. How can i make this two
>> columns....or more (see below)
>>
>
> I am sorry, but I do not understand what you want to do or what the
> problem may be.
> Can you please give more details? What exactly is being put in one  
> column?
> Please also provide the output of "sessionInfo()"
> to let us know which package versions you are using.
>
> Best regards,
> Joern
>