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DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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readGeoMx error in rowNames #28

Closed kav-ita closed 8 months ago

kav-ita commented 8 months ago

Hi Ning, I'm having issues with the readGeoMx function. I'm using R version 4.3.2 and standR_1.6.0

This is the code I run: spe <- readGeoMx(countFile, sampleAnnoFile, featureAnnoFile)

This is the error message I receive: Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed

  1. stop("duplicate 'row.names' are not allowed") 6..rowNamesDF<-(x, value = value) 5.row.names<-.data.frame(tmp, value = value) 4.row.names<-(tmp, value = value) 3.rownames<-(tmp, value = samplemeta[, colnames.as.rownames[2]]) 2.geomx_import_fun(countFile, sampleAnnoFile, featureAnnoFile, rmNegProbe, NegProbeName, colnames.as.rownames, coord.colnames) 1.readGeoMx(countFile, sampleAnnoFile, featureAnnoFile)
kav-ita commented 8 months ago

Found and solved issue with csv file; unrelated to package