HelenaLC / CATALYST

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problem with preprocessing and normalization! #405

Open yamihn opened 3 weeks ago

yamihn commented 3 weeks ago

Hi, when I run normCytof with the following command:


 res <- normCytof(sce, beads = "dvs", k = 37, dna= c(191, 193),
+                  assays = c("counts", "exprs"), overwrite = FALSE)
Identifying beads...
Computing normalization factors...
Warning messages:
1: In min(y[, dna_chs[1]]) :
  no non-missing arguments to min; returning Inf
2: In max(y[, dna_chs[1]]) :
  no non-missing arguments to max; returning -Inf

Can you help me? what does the message mean?

HelenaLC commented 3 weeks ago

R the specified dna_chs in ur data? Else u need to specify which are.

yamihn commented 3 weeks ago

In my data I see Intercalator-Ir Ir191Di Intercalator-Ir Intercalator-Ir.1 Ir193Di Intercalator-Ir

So which I have to specify? It only accepts vectors. I'm sorry I am a newbie in Cytof. moreover, is it normal my output?

plot smoothed bead intensities

Screenshot from 2024-09-26 13-46-23