[BioC] limma, spot quality weight

[Marcus Davy]

Try modfying your statement x[,"FlagA"]="A"|"B"|"C" etc to use the test
operator rather than the assignment operator.
Something like;

okred <- x[,"FlagA"]=="A" | x[,"FlagA"]=="B" | x[,"FlagA"]=="C"


Marcus


On 12/1/06 8:52 AM, "Yolande Tra" <yvtsma at rit.edu> wrote:

> Hi, 
>  
> I have cDNA array data processed through TIGR Spotfinder. I tried the
> followimg for Spot quality weigth but it did not work
>  
>  myfun <- function(x) {
> + okred <- x[,"FlagA"]="A"|"B"|"C"
> + okgreen <- x[,"FlagB"]="A"|"B"|"C"
> + as.numeric(okgreen & okred)}
>> RG <- read.maimages(filenames, wt.fun=myfun)
> Error in read.maimages(filenames, wt.fun = myfun) :
>         must specify columns for generic input
> 
> The Flags for each channel 1 and 2 are nonnumerical values A, B or C if good
> spots. They are in columns named Flag A and Flag B in each of 11 files defined
> below 
>  
>> filenames
>  [1] "IE1107_bottomGrid.mev" "IE1107_topGrid.mev"    "IE1108_bottomGrid.mev"
>  [4] "IE1109_bottomGrid.mev" "IE1109_topGrid.mev"    "IE1110_bottomGrid.mev"
>  [7] "IE1111_topGrid.mev"    "IE1113_bottomGrid.mev" "IE1113_topGrid.mev"
> [10] "IE2637_bottomGrid.mev" "IE2637_topGrid.mev"
> 
> Can anyone please help me out? Thanks.
>  
> Yolande
> 
> [[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor


______________________________________________________

The contents of this e-mail are privileged and/or confidenti...{{dropped}}