nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Issue with SPADE.driver #145

Open santoshe1 opened 3 years ago

santoshe1 commented 3 years ago

Hi,

I am facing an issue with SPADE.driver, which throws a subscript out of bounds error:

Script:
fcs<-"505333.fcs"
libraray(flowAI)
fs_clean <- flow_auto_qc(fs, output = 1)
fcs <- "fs_clean.fcs"

markers <- c("FSC-A","FSC-H","SSC-A","FITC-A","PerCP Cy55 Blue-A","Pacific Blue-A","Am Cyan-A", "APC-A", "Alexa 680-A", "APC Cy7-A", "PE Green laser-A", "PE Tx RD-A", "PE Cy5-A", "PE Cy7-A", "Qdot 655-A", "Qdot 605-A")

output_dir <- "/PENNVAX/505333/"
transforms <- flowCore::biexponentialTransform()
SPADE.driver(fcs, out_dir=output_dir, transforms = transforms, cluster_cols=markers, panels = NULL)
Downsampling file: /PENNVAX/505333/resultsQC/505333_QC.fcs
  Estimated downsampling-I progress:  0% ...
  Estimated downsampling-I progress: 100% ...
Targeting 18397 events for /PENNVAX/505333/505333_QC.fcs.density.fcs
Clustering files...

This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
Error in `*tmp*`[[4]] : subscript out of bounds

Kindly assist.

santoshe1 commented 3 years ago

I still get the same issue.