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scaffold
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Error message in scaffold analysis #5

Open Nemo2013 opened 7 years ago

Nemo2013 commented 7 years ago

Hi there, This is the first time I am using scaffold. I have got the .Rdata files and am trying to run the scaffold analysis as in the README. I keep getting an error "missing value where TRUE/FALSE needed". I have tried filling in different combinations of things in the drop down menu/tick boxes but still get this error. I have my gated fcs files in a subdirectory "gated"...

This is the print out I get in R studio - tack trace (innermost first): 89: load_attractors_from_gated_data 88: scaffold:::run_analysis_gated 81: isolate 80: renderText [/Library/Frameworks/R.framework/Versions/3.3/Resources/library/scaffold/shinyGUI/server.R#352] 79: func 78: origRenderFunc 77: output$analysisui_empty 2: runApp 1: scaffold.run

Any suggestions where I am missing this TRUE/FALSE value?

Thanks very much. Kirsten

PS. Sorry for cross posting - I initially put this in the wrong thread.

GalliES commented 6 years ago

Hi there! Did you find a solution to your problem? I am actually facing the same hurdle, with no success so far.... Anyone who could help?

KirstenMS commented 6 years ago

I didn't get round it yet but have been working on other things. I will let you know if I solve it!

pfgherardini commented 6 years ago

Hi,

Apologies for the late reply. Have you been able to solve this?

LKBlum commented 6 years ago

Hi, I am also having this problem. Has anyone solved it yet? Thank you!

Warning: Error in if: missing value where TRUE/FALSE needed 107: load_attractors_from_gated_data 106: scaffold:::run_analysis_gated 93: renderText [C:\Users\lblum\Documents\R\win-library\3.5\scaffold\shinyGUI/server.R#352] 92: func 79: origRenderFunc 78: output$analysisui_empty 2: runApp 1: scaffold.run

LKBlum commented 6 years ago

I believe I found the problem at line 78 of scaffold/blob/master/R/force_directed_matching_gated.R, in the load_attractors_from_gated_data function: If(!all(pData(parameters(fcs))$desc == " ")).

In my file pData(parameters(fcs))$desc are all NA, not “ ”, so that was breaking it.

It worked for me after adding descriptions, e.g.: library(flowCore) descriptions <- c("Time", "SSC-H", "SSC-A", "FSC-H", "FSC-A", "CD3", "CD14", "CD16") for(file in [all sample and gating fcs files]){ fcsfile = read.FCS(file) pData(parameters(fcsfile))$desc <- descriptions write.FCS(fcsfile, paste0("label_", file)) }