[BioC] limma: fold-changes corrected for dye-effect

[karsten_hokamp at sfu.ca]

Hi list,

In the limma userguide it says at the end of section "8.1.2 Dye Swaps" 
(page 34): "The fold changes and significant tests in this list are 
corrected for dye-effects."

When I process microarray data with and without dye-effect specified I can
see the p-values being corrected, but the logFC values as reported by
topTable stay the same.

Below are the steps I carried out on a small artificial sample data set:

> files = c('val1', 'val2', 'val3', 'val4')
> RG = read.maimages(files, columns=list(G="F1",R="F2",Gb="B1",Rb="B2"),
+ annotation=c("Spot"))
Read val1
Read val2
Read val3
Read val4
> ma = MA.RG(RG, bc.method="none")
> ma$M
     val1 val2 val3 val4
[1,]   -3    1   -1    1
[2,]    1   -2    1   -1
[3,]    4   -4    2   -4
[4,]    0    0    0    1
[5,]    4   -6    4   -6
>
> design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1))
> design2 <- cbind(MUvsWT=c(1,-1,1,-1))
> fit <- lmFit(ma, design)
> fit <- eBayes(fit)
> fit2 <- lmFit(ma, design2)
> fit2 <- eBayes(fit2)
> topTable(fit, coef="DyeEffect")
  logFC AveExpr           t      P.Value    adj.P.Val         B
5 -1.00   5.500 -124.500939 1.338072e-05 0.0000669036  4.801725
1 -0.50   1.750   -1.091256 3.731143e-01 0.3732967729 -8.968102
3 -0.50   4.250   -1.091256 3.731143e-01 0.3732967729 -8.968102
2 -0.25   7.375   -1.090753 3.732968e-01 0.3732967729 -8.968621
4  0.25   7.125    1.090753 3.732968e-01 0.3732967729 -8.968621
> topTable(fit, coef="MUvsWT")
  logFC AveExpr          t      P.Value    adj.P.Val         B
5  5.00   5.500 622.504696 2.892709e-07 1.446354e-06  7.651719
3  3.50   4.250   7.638791 9.962634e-03 2.490659e-02 -4.415323
2  1.25   7.375   5.453766 2.148516e-02 3.580860e-02 -5.491825
1 -1.50   1.750  -3.273768 6.461363e-02 8.076704e-02 -7.008591
4 -0.25   7.125  -1.090753 3.732968e-01 3.732968e-01 -9.206043
> topTable(fit2)
  logFC AveExpr          t      P.Value    adj.P.Val         B
5  5.00   5.500 10.6609570 1.549942e-26 7.749712e-26 49.311955
3  3.50   4.250  7.4626699 8.478657e-14 2.119664e-13 20.722709
1 -1.50   1.750 -3.1982871 1.382466e-03 2.304109e-03 -1.700230
2  1.25   7.375  2.6652393 7.693357e-03 9.616696e-03 -3.241807
4 -0.25   7.125 -0.5330479 5.940005e-01 5.940005e-01 -6.605248
> sessionInfo()
R version 2.4.1 (2006-12-18)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"

other attached packages:
   limma
"2.9.17"


Am I doing something wrong?

Thanks for any help,

	Karsten