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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Error in prepData #351

Closed FRLab closed 1 year ago

FRLab commented 1 year ago

Hello,

I've been using CATALYST for a long time now, and I have suddenly an error occurring when prepData is running.

I get this classical error

Error in prepData(data_clean, panel, meta, features = panel$fcs_colname, : panel[[panel_cols$channel]] %in% colnames(fs) are not all TRUE

The problem is that I checked everything and, more, I tried to run previous codes that were normally running and are published, and the same error is happening. 

FCSdata <- flowCore::read.flowSet(path=FCSdir, emptyValue = F, column.pattern = "Cd", invert.pattern = T)
sce <- CATALYST::prepData(FCSdata, panel=panel, md=meta, features=panel$fcs_colname, transform=T, panel_cols = list(channel = "fcs_colname", antigen = "antigen", class = "marker_class"),
                          md_cols = list(file = "file_name", id = "sample_id", factors = c("condition",
                                                                                           "patient_id")))

panel$fcs_colname[!panel$fcs_colname %in% colnames(FCSdata)] is giving character(0)

all(panel$fcs_colname %in% colnames(FCSdata)) is giving TRUE all(names(FCSdata@frames) %in% meta$file_name) is giving TRUE

I reinstall CATALYST etc but nothing is fixing the bug.

Have you ever had this issue?

Thank you very much !

Quentin

FRLab commented 1 year ago

Sorry for this I finally find that I changed the environment of the function by mistake that was causing the issue.