[BioC] Question about Correlation (Limma package)
Gordon Smyth
smyth at wehi.edu.au
Fri Apr 8 13:05:14 CEST 2005
At 08:01 PM 8/04/2005, bioconductor-request at stat.math.ethz.ch wrote:
>Date: Thu, 07 Apr 2005 12:28:58 -0400
>From: yzou1971 at netscape.net
>Subject: [BioC] Question about Correlation (Limma package)
>To: bioconductor at stat.math.ethz.ch
>
>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"?
Yes, of course, that is what duplicateCorrelation() is provided for. Unless
you want to just use the default correlation value.
I prefer to separate the correlation estimation and the linear model fit
into two separate functions because (i) both steps can be quite time
consuming and (ii) I want you to look at the correlation value for
reasonablenes before entering it into the linear model fit.
>If I should use "duplicateCorrelation" only when there are duplicate spots
>within array?
Yes, naturally. If there are no duplicates, there is no correlation to
estimate.
>(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.
So you've done a lot of experiments and have decided that 0.75 must be the
default value for 'correlation'. An alternate and less circuitious path
might have been to read the help page. Typing args(lmFit) or ?lmFit would
have told you immediately that 0.75 is the default value.
Gordon
>Thanks
>
>yi
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