[BioC] duplicateCorrelation

[Gordon Smyth]

Dear Hua,

At 09:57 AM 3/12/2005, Hua Weng wrote:
>Hi all:
>
>I found a strange situation. Before I did normalization, the correlation
>within slide is pretty high, 0.5009. After I did normalization, the
>correlation goes down to 0.1672.

Doesn't seem at all strange to me. That's what is supposed to happen.

You can't really expect anything sensible from standard deviations or 
correlations on un-normalized data.

>  I am pretty sure spacing between duplicates
>is correct. Does it mean the normalization method is not correct?

No, quite the opposite.

BTW, your question would be more meaningful if you tried to explain why you 
find the behaviour surprising, and what you expected instead.

Best wishes
Gordon

>  I am using
>printtiploess normalization.
>
> > cor <- duplicateCorrelation(RG, design, ndups=6, spacing=1152)
> > cor$consensus.correlation
>[1] 0.5009
> > cor <- duplicateCorrelation(MA.norm, design, ndups=6, spacing=1152)
> > cor$consensus.correlation
>[1] 0.1672
>
>I highly appreciate any comments.
>
>Hua Weng