Hello,

I've been trying to read and analyze some ArrayVision filesusing LIMMA and I
always get the same problem. I am using R 2.2.1 and I updated my LIMMA to
the last version today. So far my code is very simple (the errors follow
below the code causing it):

> targets <- readTargets("targets.txt")
> data <- read.maimages(targets$FileName, source="arrayvision")

Read 01_WG_WR_600_900_flag.txt
Read 02_PG_PR_650_900_flag.txt
Read 03_PG_PR_650_900_flag.txt
Read 26_WG_WR_0651_flag.txt
Read 28_WG_WR_670_900.txt
Read 04_PG_PR_650_800.txt
Read 05_PG_PR_650_900.txt
Warning message:
number of items read is not a multiple of the number of columns

> data$genes <- readGAL("cere32pinsJAN04.gal")
> data$printer <- getLayout(data$genes)
> MA<- normalizeWithinArrays(data,  method="l")
> library(convert)
> data.marray <- as(data, "marrayRaw")

Error in checkSlotAssignment(object, name, value) :
assignment of an object of class "integer" is not valid for slot 'maGf' in
an object of class "marrayRaw"; is(value, "matrix") is not TRUE

When I try to normalize the data using a printtip method as for instance:
>MA<- normalizeWithinArrays(data)
I get the following error:
Error in switch(method, loess = { : printer layout information does not
match M row dimension

The targets.txt file is like this:
SlideNumber    FileName    cy3    cy5
01    01_WG_WR_600_900_flag.txt    WR    WG
02    02_PG_PR_650_900_flag.txt    PR    PG
03    03_PG_PR_650_900_flag.txt    PR    PG
26    26_WG_WR_0651_flag.txt    WG    WR
28    28_WG_WR_670_900.txt    WG    WR
04    04_PG_PR_650_800.txt    PG    PR
05    05_PG_PR_650_900.txt    PG    PR
 Anyone can help me?

Best regards,
-- 
Michael Waisberg
R. Nicaragua 443/701, Sion
Belo Horizonte, MG
Brazil
30320-050


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