shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
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@acaa643d
Last seen 4 days ago
Canada

I combined two arrays using combinedArray() function from Minfi. I want to visualize the raw results using shinyMethyl however I run into an issue. i see someone posted something similar in 2017 (https://github.com/Jfortin1/shinyMethyl/issues/2) and it was resolved so I'm confused - any help would be appreciated.

combined_array <- combineArrays(rgset_450,rgset_850,outType="IlluminaHumanMethylation450k") [convertArray] Casting as IlluminaHumanMethylation450k Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylationEPICmanifest

library(shinyMethyl) Loading required package: shiny

summary <- shinySummarize(combined_array) [shinySummarize] Extracting Red and Green channels [shinySummarize] Raw preprocessing [shinySummarize] Mapping to genome Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 [shinySummarize] Computing quantiles [shinySummarize] Computing principal components

summary Object: shinyMethylSet Number of samples: 137 Phenotype: 22 covariates Origin object: RGChannelSet Array: IlluminaHumanMethylation450k

runShinyMethyl(summary) Error in object@greenControls[[i]][, o] : incorrect number of dimensions

shinyMethyl minfi • 79 views
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