[BioC] results of justPlier vs. RMA

[He, Yiwen (NIH/CIT) [C]]

Hi,
When comparing the results of RMA from the affy package and justPlier
from the plier package, I found that the summarized data are clustered
very differently. The cluster of the RMA results is very close to MAS5
values, showing 5 groups. However, PLIER results show a very different
and strange clustering pattern, almost like using single linkage. (See
attached figure)

I used Pearson correlation coefficient distance and average linkage for
all clustering.

I remember attending a web talk about PLIER and the speaker mentioned
post-processing scaling in PLIER. Is that done in justPlier? Or is this
an additional step that needs to follow justPlier? Or is it something
else?

Thank you for your help!

Here is my code:
> sessionInfo()
R version 2.4.0 (2006-10-03)
sparc-sun-solaris2.8

locale:
C

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

other attached packages:
   plier     affy   affyio  Biobase
 "1.4.0" "1.12.0"  "1.2.0" "1.12.2"


> eset1 <- rma(myData)
> exprs(eset1) <- 2^exprs(eset1)

> eset2 <- justPlier(myData, normalize=T)
> exprs(eset2) <- 2^exprs(eset2)

Yiwen He