[BioC] Dup correlation in single-channel analysis?- technical rep

[Heather de Glanville]

Dear Bioconductor,

I am working with a loop design with both biological and technical 
replication, and am having difficulty incorporating both types of 
replication appropriately. I am looking at the both strain and the 
treatment level effects, will make most all possible contrasts, and 
would like to test this over the biorep error.

My experiment follows, with 6 different strain/treatments 
(CD,CW,HD,HW,VD,VW), 3 bio reps per strain/treat (1,2,3) and 2 techreps 
per biorep.

Slide

	

Cy3

	

Cy5

1

	

VW3

	

HW2

2

	

HW2

	

HD1

3

	

HD2

	

HW1

4

	

VD3

	

HD2

5

	

CD1

	

HD3

6

	

CW1

	

HW3

7

	

VW2

	

VD1

8

	

VD2

	

VW1

9

	

CD3

	

VD2

10

	

CW3

	

VW2

11

	

HW1

	

VW3

12

	

HD3

	

VD3

13

	

CW2

	

CD1

14

	

HD1

	

CD2

15

	

CD2

	

CW1

16

	

VW1

	

CW2

17

	

VD1

	

CD3

18

	

HW3

	

CW3

It seems like I could use single-channel analysis, and use duplicate 
correlation to indicate which file and channels are the technical reps. 
I am getting an error when attempting to do this

targets2 <- targetsA2C(targets)
u <- unique(targets2$Target)
f <- factor(targets2$Target, levels=u)
design <- model.matrix(~0+f)
colnames(design) <- u
biolrep 
<-c(11,18,7,11,10,8,8,15,9,1,12,4,13,17,16,14,14,3,17,6,18,10,15,9,1,5,2,7,4,2,5,16,3,13,6,12)
corfit <-duplicateCorrelation(MAAq, ndups=1, block=biolrep)
fit <- lmFit(MAAq, block=biolrep, cor=corfit$consensus)

Error in gls.series(y, design = design, ndups = ndups, spacing = spacing, :

Length of block does not match number of arrays

Thank you for looking over this case. I’m struggling with the R program 
in general, so perhaps that accounts for some of my general confusion.

Sincerely,

Heather de Glanville