[BioC] preprocessing for tiling arrays (preprocessCore package)

[Ben Bolstad]

the issue with rma.background.correct is it failing to return the
background corrected matrix when copy =TRUE (copy=FALSE will work). This
is a genuine bug. It has been addressed in the devel-branch
(http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/preprocessCore/) at 1.3.1.
Unfortunately, I did not patch the release branch with the fix (I should
do so).

Ben


On Mon, 2008-07-21 at 11:13 -0600, Ann Hess wrote:
> I would like to perform RMA style preprocessing for tiling arrays.  Based 
> on previous discussion (thanks Ben and Jim!), it seems that the functions 
> rma.background.correct() and normalize.quantiles() from the 
> preprocessCore package are the easiest way to accomplish this.
> 
> First of all, I am having trouble getting the functions to work.  The 
> rma.background.correct() function seems to be returning the original 
> values.  The normalize.quantiles() function does something to the data, 
> but the medians are not equal across arrays (which I would have expected 
> from quantiles normalization).
> 
> Secondly, I wanted to verify that to most closely match the RMA algorithm, 
> I should (1) restrict to PM values (2) background correct, (3) normalize, 
> then (4) log2 transform. Is this correct?
> 
> The code (using Canine2 arrays for quicker experimentation) and 
> sessionInfo are below.
> 
> Ann
> 
> **************************************
> 
> > library(affy)
> > library(preprocessCore)
> > AllArrays<-ReadAffy()
> > PM<-pm(AllArrays)
> > dim(PM)
> [1] 473162     15
> > PM[1:10,1:5]
>         RB1.CEL RB10.CEL RB11.CEL RB12.CEL RB13.CEL
> 571209     134       52       56       67      309
> 571210     151       63       78       85      587
> 571211     388      116      134      129     1396
> 571212     215       56       68       67      530
> 571213      83       41       42       47      131
> 571214      83       42       41       50      148
> 571215     107       43       42       63      194
> 571216     216       48       69       83      620
> 571217     254       61       80       79      876
> 571218     131       42       61       47      246
> > BG<-rma.background.correct(PM)
> > dim(BG)
> [1] 473162     15
> > BG[1:10,1:5]
>         RB1.CEL RB10.CEL RB11.CEL RB12.CEL RB13.CEL
> 571209     134       52       56       67      309
> 571210     151       63       78       85      587
> 571211     388      116      134      129     1396
> 571212     215       56       68       67      530
> 571213      83       41       42       47      131
> 571214      83       42       41       50      148
> 571215     107       43       42       63      194
> 571216     216       48       69       83      620
> 571217     254       61       80       79      876
> 571218     131       42       61       47      246
> 
> > Norm<-normalize.quantiles(BG)
> > dim(Norm)
> [1] 473162     15
> > Norm[1:10,1:5]
>            [,1]      [,2]      [,3]      [,4]     [,5]
>   [1,] 128.4667 143.40000 114.06667  332.7333 230.0000
>   [2,] 145.0000 202.66667 188.80000  560.2000 413.3333
>   [3,] 383.6000 480.93333 368.73333 1110.5000 936.6333
>   [4,] 208.6000 164.80000 155.20000  332.7333 375.8667
>   [5,]  79.6000  84.40000  65.26667  103.0667 108.0667
>   [6,]  79.6000  89.73333  62.00000  131.9333 120.0000
>   [7,] 102.3333  95.26667  65.26667  283.1333 151.9333
>   [8,] 209.4000 122.13333 158.80000  534.5333 435.6000
>   [9,] 247.5333 191.73333 195.80000  482.5333 602.5667
> [10,] 125.7333  89.73333 131.33333  103.0667 187.9333
> 
> > apply(Norm,2,median)
>   [1] 104.4667 106.1333 103.7333 103.0667 103.9333 104.2000 104.4667
>   [8] 104.4667 104.8000 104.0667 103.6667 103.6667 107.2000 106.0000
> [15] 103.6667
> 
> > apply(PM,2,median)
>   RB1.CEL RB10.CEL RB11.CEL RB12.CEL RB13.CEL RB14.CEL RB15.CEL
>       109       45       53       47      125      355      191
>   RB2.CEL  RB3.CEL  RB4.CEL  RB5.CEL  RB6.CEL  RB7.CEL  RB8.CEL
>        93       86       93      113      105       42       53
>   RB9.CEL
>        53
> 
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> [7] methods   base
> 
> other attached packages:
> [1] canine2cdf_2.2.0     affy_1.18.2          preprocessCore_1.2.0
> [4] affyio_1.8.0         Biobase_2.0.1
> 
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