Dear all,
 
I am trying to use the Kooperberg model-based background correction in my data but it is not working. Apparently it can only take the values in the columns with the following names:  other.columns=c("F635 SD","B635 SD","F532 SD","B532 SD","B532 Mean","B635 Mean","F Pixels","B Pixels").
But I am using other wavelengths (647 instead of 635 and 555 instead of 532) and I would also like to use another statistic instead of B mean. Is there a way to do that?
 
Here is my code and the error message:
 
>  columns <- list(Rf = "F647 Median", Gf = "F555 Median", Rb = "B647", Gb = "B555")
> other.columns=c("F647 SD","B647 SD","F555 SD","B555 SD","B555 Mean","B647 Mean","F Pixels","B Pixels")
> RG <- read.maimages(fnames, source="genepix.custom", path=datadir, ext="gpr", columns=columns, other.columns=other.columns)
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019750_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019767_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019774_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019781_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019798_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019804_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019811_121506.gpr 
Custom background: MorphologicalClosingFollowedByOpening 
Read C:/CGH_self_self_hybr/intensities/019835_121506.gpr 
> RGmodel <- kooperberg(RG)
Error in kooperberg(RG) : 
Data missing from RG$other: re-run read.maimages with
 other=c("F635 SD","B635 SD","F532 SD","B532 SD","B532 Mean","B635 Mean","F Pixels","B Pixels")

 
Best regards,
João Fadista


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