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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
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Consolidate and summarize #40

Closed tanerhf closed 4 years ago

tanerhf commented 4 years ago

Hello,

I am trying to consolidate my merge files, and am having some issues. When I input all of them together I get a warning:

Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "", and the latter is "Cell seg data summary". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check. Joining, by = "Slide ID" Joining, by = "Slide ID" Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "", and the latter is "Cell seg data summary". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check. Warning: Error in split_phenotypes: No positive phenotypes found.

The files are not consolidated. I ran the files one at a time to see what happens. I am able to get separate files this way and all my populations of interested have the (+).

Any help would be greatly appreciated!

Hulya

SDJ7007 commented 3 years ago

Hey Did you get any answer for this? I am receiving the same error. Thank you. -Shweta Johari

AB-Kent commented 3 years ago

The warnings about the vignette title were fixed long ago; please update to the latest phenoptr and phenoptrReports. The consolidation app does require that positive phenotypes are represented in the data being consolidated.