[BioC] Limma - background correction

[Matt Ritchie]

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

João 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,
>João Fadista
>