Error in readGeoMx qith rmNegProbe = FALSE

DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R

https://davislaboratory.github.io/standR/

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Error in readGeoMx qith rmNegProbe = FALSE #18

Closed Sigmatilde closed 10 months ago

Sigmatilde commented 1 year ago

I am trying to run the cellular deconvolution analysis and the readGeoMx(countFile, sampleAnnoFile, featureAnnoFile, rmNegProbe = FALSE) is generating the error:

Warning: non-unique value when setting 'row.names': ‘NegProbe-WTX’
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed

ningbioinfo commented 1 year ago

Hi @Sigmatilde , there are multiple NegProbe-WTX probes in your data, if you want to retain the negative probes, I would suggest you to change the name of them, e.g. NegProbe-WTX1, NegProbe-WTX2, NegProbe-WTX3.. etc.