[BioC] Limma

[Wayne Yu]

I was using "separate channel analysis of two-color data" for data from
17 Agilent 44K oligomer arrays and had error massages for wihich I
copied and pasted below:

> targets2.sc
     channel.col FileNames  Target
1.1            1   29N.txt ant.con
1.2            2   29N.txt lat.con
2.1            1  273N.txt lat.con
2.2            2  273N.txt ant.con
3.1            1  283N.txt lat.con
3.2            2  283N.txt ant.con
4.1            1  267N.txt ant.con
4.2            2  267N.txt lat.con
5.1            1  281N.txt lat.con
5.2            2  281N.txt ant.con
6.1            1  289N.txt lat.con
6.2            2  289N.txt ant.con
7.1            1  103R.txt ant.res
7.2            2  103R.txt lat.res
8.1            1  105R.txt lat.res
8.2            2  105R.txt ant.res
9.1            1  104R.txt ant.res
9.2            2  104R.txt lat.res
10.1           1  213R.txt lat.res
10.2           2  213R.txt ant.res
11.1           1  338R.txt lat.res
11.2           2  338R.txt ant.res
12.1           1    2D.txt ant.dys
12.2           2    2D.txt lat.dys
13.1           1  101D.txt lat.dys
13.2           2  101D.txt ant.dys
14.1           1  425D.txt lat.dys
14.2           2  425D.txt ant.dys
15.1           1   53D.txt ant.dys
15.2           2   53D.txt lat.dys
16.1           1  424D.txt lat.dys
16.2           2  424D.txt ant.dys
17.1           1 53D_2.txt lat.dys
17.2           2 53D_2.txt ant.dys

> u <- unique(targets2.sc$Target)
> f <- factor(targets2.sc$target, levels=u)
> design <- model.matrix(~0+f)
Warning message:
is.na() applied to non-(list or vector) in: is.na(rows) 
> colnames(design) <- u
               
> dim(design)
[1] 0 6
> dim(f)
NULL

> corfit <- intraSpotCorrelation(MA2, design)
Error: couldn't find function "intraSpotCorrelation"

> fit <- lmscFit(MA2, design, correlation=corfit$consensus)
Error in lmscFit(MA2, design, correlation = corfit$consensus) : 
        The number of rows of the design matrix should match the number
of channel intensities, i.e., twice the number of arrays

> ?intraSopt> corfit <- intraspotCorrelation(MA2, design)
Error in intraspotCorrelation(MA2, design) : 
        The number of rows of the design matrix should match the number
of channel intensities, i.e., twice the number of arrays

********************************

It seems the codes for design file is wrong. I looked model.matrix but
didn't get clues. Can you help me out? Thanks.

Wayne