[BioC] vsn + backgroundSubtract

[DAVID ARTETA GARCIA]

Dear list, please apologise for not providing enough information.

> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

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

other attached packages:
  [1] arrayQuality_1.18.0  RColorBrewer_1.0-2   gridBase_0.4-3        
hexbin_1.14.0        convert_1.16.0       marray_1.18.0        vsn_3.6.0
  [8] limma_2.14.0         lattice_0.17-6       affy_1.18.0           
preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.0


I have 12 one-color gpr files. These were loaded using limma´s read.maimages()

> data = read.maimages(filenames,source="genepix")
Read 0023.gpr
Read 0024.gpr
Read 0025.gpr
.
.

data
An object of class "RGList"

I then transformed R and Rg to NULL as suggested on this list (after  
searching in the archives).

I actually tried vsn normalisation of G values using the most recent  
vsn2() function ( I guess I could have also used justvsn()). If I am  
not wrong, vsn2 can take a matrix as argument:

data.norm = vsn2(data2$G)
vsn: 2352 x 12 matrix (1 stratum).   0% done.
  14% done.
  28% done.
  42% done.
  57% done.
  71% done.
  85% done.
100% done.
Please use 'meanSdPlot' to verify the fit.

but I also wanted to check wether there was an improvement correcting  
for backgroung effects since I can see a spatial trend on some of the  
chips. I read on the vsn vignette that the argument  
"backgroundsubtract" to justvsn might take care of this trend, but of  
course, the function could not find "R":

data.vsn_b<-justvsn(data2,backgroundsubtract=TRUE)
Error in eval(expr, envir, enclos) : object "R" not found
Error in is(object, Cl) :
   error in evaluating the argument 'x' in selecting a method for  
function 'vsn2'

Maybe I should leave R and Rg as they are (all 0´s) instead of NULL-ing them?

I haven´t tried converting to an ExpressionSet which I thought was  
mainly for affy data, but how can I handle both the foreground G and  
background Gb data in the ExpressionSet? I haven´t confronted this  
matter before.

Thanks,

D.

Quoting Wolfgang Huber <huber at ebi.ac.uk>:
>
>
> Dear David,
>
> please provide the output of sessionInfo() and a reproducible example,
> otherwise it is difficult to give a concrete reply.
>
> Also, please use the function "vsn2" instead of "vsn" (both in the
> package vsn).
>
> From your message it appears (sorry if my guess is wrong - see above)
> as if you use an RGList for one color data - which, if true, would be
> weird. Have you tried putting the data into an ExpressionSet and then
> calling vsn2/justvsn on that?
>
>  Best wishes
> 	Wolfgang
>
>
> -- 
> ----------------------------------------------------
> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>
>
> DAVID ARTETA GARCIA wrote:
>> Hi Wolfgang and list,
>>
>> Is it possible to do vsn() or justvsn() with   
>> backgroundSubtract=TRUE for a one-color genepix chip? I tried and   
>> received an error saying that "object R was not found". Could I   
>> fool the function duplicating G and Gb into R and Rb or will the   
>> normalisation result then be modified and get erroneous output??
>>
>>
>> Thanks for your help,
>>
>>
>> David
>>
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