[BioC] negative correlation?

[Naomi Altman]

Oops again.  The limma manual explains this.  Too quick on the send 
button as usual.

--Naomi

At 01:24 PM 6/29/2011, Naomi Altman wrote:
>I am running limma 2.8 on a technical replicate dye-swap 
>design.  Here is my design matrix:
>
>(Intercept) as.factor(targets$time)24h as.factor(targets$time)4h 
>as.factor(targets$time)8h
>1           -1                          0                         0 
>                      0
>2            1                          0                         0 
>                      0
>3           -1                          0                         0 
>                      0
>4            1                          0                         0 
>                      0
>5           -1                          0                         1 
>                      0
>6            1                          0                         1 
>                      0
>7           -1                          0                         1 
>                      0
>8            1                          0                         1 
>                      0
>9           -1                          0                         0 
>                      1
>10           1                          0                         0 
>                      1
>11          -1                          0                         0 
>                      1
>12           1                          0                         0 
>                      1
>13          -1                          1                         0 
>                      0
>14           1                          1                         0 
>                      0
>15          -1                          1                         0 
>                      0
>16           1                          1                         0 
>                      0
>
>
>corfit <- duplicateCorrelation(MA, design=designTimeR,ndups = 1, 
>block = targets$biorep)
>
>targets$biorep
>  [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8
>
>
> > corfit$con
>[1] -0.3414428
>
>Why am I getting a negative correlation between bio reps?  Is this 
>expected due to the dye swap?
>
>--Naomi
>
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