[BioC] error in Limma normalization with bc.method="normexp"

[Caimiao Wei]

 Dear all,

I got this error while I was trying to normalize (first within arrays, then 
between arrays) Agilent arrays  using these code lines (R2.0.0, bioConductor 
1.5, Windows XP):

> #########normalize within arrays



> MA<-normalizeWithinArrays(RG, method="loess", bc.method="normexp", 
> offset=2)

Corrected array 1

Corrected array 2

Corrected array 3

Corrected array 4

Corrected array 5

Corrected array 6

Corrected array 7

Corrected array 8

Corrected array 9

Corrected array 10

Corrected array 11

Corrected array 12

Corrected array 13

Corrected array 14

Corrected array 15

Corrected array 16

Corrected array 17

Corrected array 18

Corrected array 19

Corrected array 20

Corrected array 21

Corrected array 22

Corrected array 23

Corrected array 24

>







> #########normalize between arrays

> MA.b=normalizeBetweenArrays(MA, method="quantile")

Error in xy.coords(x, y) : x and y lengths differ



I found that MA$A and MA$M contain a few columns with all "NA" values.



if I replace bc.method="normexp" with bc.method="half", everything look 
fine.



if I did not use the "bg.method" option at all, then many elements (but not 
all) of the columns metioned above (all "NA") are "NA".



Thanks



Caimiao