[BioC] Question about Correlation (Limma package)

[yzou1971 at netscape.net]

Hi,

I have 4 replicate slides. Within each slide, there are 3 replicate spots for each gene. After doing the within Array normalization, I ran lmFit(limma) with two ways and get different correlation values as following:

(1)lmFit1 

> ADlmFit1 <- lmFit(ADraw.NormWA, ADdesign, ndups=3)
> ADlmFit1$correlation
[1] 0.75


(2)lmFit2

> cor <- duplicateCorrelation(ADraw.NormWA,ADdesign, ndups=3)
> cor$consensus.correlation
[1] 0.5548806
> ADlmFit2 <- lmFit(ADraw.NormWA,ADdesign, ndups=3, correlation=cor$consensus.correlation)
> ADlmFit2$correlation
[1] 0.5548806

Questions:

(1) Why I got different correlation value if I ran "duplicateCorrelation" firstly? For my slides with diplicate spots, Should I always calculate the correlation value using "duplicateCorrelation" before running "lmFit"? If I should use "duplicateCorrelation" only when there are duplicate spots within array?


(2) If I ran "lmFit" only I always got correlation 0.75, I also ran other slides and got the same correlation 0.75, It looks that 0.75 is the default correlation value if I didn't give specific value to correlation. Why the "lmFit" always give correlation 0.75 for different data analysis? It looks not reasonable. I'm very confused. 

Thanks

yi


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