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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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runPCA error : Error in if (R < eps2) { : missing value where TRUE/FALSE needed #499

Closed pillar-github closed 1 year ago

pillar-github commented 1 year ago

stereo_go <- stereo_go %>% runPCA(expression_values = 'scaled', feats_to_use = 'hvf')

"hvf" was found in the feats metadata information and will be used to select highly variable features class of selected matrix: dgeMatrix

Error in if (R < eps2) { : missing value where TRUE/FALSE needed

Ed2uiz commented 1 year ago

Hey @pillar-github. Could you share which version of Giotto you are using? Also, did you modify the Stereo-seq tutorial code in anyway (e.g. different input data or different parameters upstream of runPCA)?

Ed2uiz commented 1 year ago

Hey @pillar-github I've double-checked the Stereo-seq tutorial and I cannot reproduce your error nor I have seen this error before. My guess is that you have modified the upstream commands from stereo_go <- stereo_go %>% runPCA(expression_values = 'scaled', feats_to_use = 'hvf') leading to the error. Please open another issue if you need further help, and be sure to share output of sessionInfo()and any upstream steps of your code.