Error in quantro function
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Entering edit mode
6.5 years ago
cge • 0

Hi,

I am using the function "quantro" (library R-quantro) to test the distribution of beta values among cases and controls to assess if it is necessary perform the quantile normalization. Test data provided in the vignette worked, but when I try with my data I get this error: 

qtest <- quantro(object = MetDataset, groupFactor = Status$Status)
[quantro] All median values equal. No ANOVA performed. 
                    No median normalization.
[quantro] Calculating the quantro test statistic.
Error in Fnik[, which(groupFactor %in% x)] : 
  incorrect number of dimensions

Anyone did struggle with this? In the beginning I thought it was just an error of the number of cases/controls in the groupFactor object, but it unfornunately it wasn't.

Thanks

SP

 

quantro methylation normalization • 1.4k views
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Entering edit mode
4.1 years ago
said3427 ▴ 100

Late response, but I just got the same error.

You have to remove rows containing NaNs

Try:

qtest <- quantro(object = MetDataset[complete.cases(MetDataset),], groupFactor = Status$Status)
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