[BioC] reproducing dChip expression measure

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Thu Apr 7 17:01:28 CEST 2005

I am trying to reproduce the dChip expression measure from the dChip
software with BioConductor packages. I am aware that dChip is not open
source but I would like to get as close as I can. Thus, I compare the
dChip expression measure from both softwares applied on a small datasets
of 12 arrays with approximately 16000 probesets.

Going through mailing archive I found that I can use the following
combinations of values for parameters to feed through expresso

	 model	pmcorrect.method   bgcorrect.method 
	 1        "pmonly"   	     "none"
	 2        "subtractmm"       "none"
	 3 	  "pmonly"    	     "mas"
	 4     	  "subtractmm"       "mas"

with the following generic incantation to expresso :

  expresso( ReadAffy(), normalize.method="invariantset", 
            bgcorrect.method=???, pmcorrect.method=???,

The correlation of the values are high and similar ( around 0.90 ). I
ahve attached both the scatterplot and hexbin of expression measures
from these two softwares under different models with the line of
identity in red. It suggests that :

a) Majority of the values are concentrated in the lower regions
b) The appears to be highly correlated values at higher end but they are
not perfectly identical
c) the MM subtracted data gives more dis-agreement at lower range but
much closer to line of identity at higher range
d) mas5 background correction does not appear to make much difference

Can other members of the list comment on 
a) if they seen similar findings
b) if these results are expected and sensibility
c) what else can I try to increase the reproducibility 

Eventually I plan on applying BioConductor's version of dChip expression
measure to few other datasets, so it would be useful to use the most
reproducible version from BioConductor.

Thank you very much.

Regards, Adai

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