[BioC] high poportion of identical expression measure with RMA and 3 arrays (addendum)

[Adaikalavan Ramasamy]

Here are the results for GC-RMA for the same datasets as below :

# Dataset 1
> print( 100*v )
 [1]         NA 3.54888484 5.62491233 0.00000000 0.07013606 0.00000000
 [7] 0.00000000 0.00000000 0.00000000 0.00000000


# Dataset 2
> print( 100*v )
 [1]       NA 0.000000 3.366337 0.000000 0.000000 0.000000 0.000000
0.000000
 [9] 0.000000 0.000000


# Dataset 3
> print( 100*v )
 [1] NA 0.1077054 9.0562312 0.0000000 0.1750213 0.0000000 0.0000000
 [8] 0.0000000 0.0000000 0.0000000



On Mon, 2004-09-13 at 18:12, Adaikalavan Ramasamy wrote:
> I was pondering about the issue of minimum number of required arrays for
> RMA and GCRMA when I came across a thread by James MacDonald
> http://files.protsuggest.org/biocond/html/3347.html. He mentioned that
> median polish has a peculiar feature that returned identical values for
> odd number of arrays, especially 3 arrays. I am not sure if this issue
> has been addressed since but here is some empirical evidence to support
> this in case anyone is interested.
> 
> ### Codes ###
> 
> library(affy)
> v <- rep(NA, 10)
> 
> for(i in 2:10){
>   a <- exprs( justRMA( filenames=list.celfiles()[1:i] ))
>   v[i] <- mean( apply(a, 1, var) == 0 )  # proportion identical
>   gc(); print(i)
> }
> 100*v
> 
> 
> ### Results ###
> 
> # Dataset 1 : hu6800 (west)
> > 100 * v
>  [1]         NA  0.0000000 13.1434984  0.0000000  0.1262449  0.0000000
>  [7]  0.0000000  0.0000000  0.0000000  0.0000000
> 
> # Dataset 2 : hgu-95av2 (febbo)
> > 100 * v
>  [1] NA 0.007920792 7.912871287 0.000000000 0.095049505 0.000000000
>  [7] 0.000000000 0.000000000 0.000000000 0.000000000
> 
> # Dataset 3 : HGU-133A (pga)
> > 100 * v
>  [1]         NA  1.5348023 16.0750348  0.0000000  0.3590181  0.0000000
>  [7]  0.0000000  0.0000000  0.0000000  0.0000000
> 
> 
> When there are 3 arrays, there is a high proportion of probesets with
> identical values (i.e. zero variance). I am trying to see if the same
> effect can be seen with justGCRMA.
> 
> misc : affy 1.4.32, gcrma 1.1.0, R-1.9.0 (12/04/2004) and FC 2.
> 
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