Dear Joao,
The kooperberg function is expecting the data stored in RG$other to
have
certain names, which are slightly different in your data set on
account
of the non-standard wavelengths (647nm and 555nm). As a quick fix,
rename the items in RG$other to the standard ones:
names(RG$other) <- c("F635 SD","B635 SD","F532 SD","B532 SD","B532
Mean","B635 Mean",
"F Pixels","B Pixels")
Now run kooperberg() as before
RGmodel <- kooperberg(RG)
This should get you going again. Best wishes,
Matt
Jo?o Fadista wrote:
>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,
>Jo?o Fadista
>
