Error when fitting the compass model

[quinnpeters]

When I try to fit the COMPASS Model with a large compass container, I get the following error which I cannot figure out how to solve:

fit <- COMPASS(CC_comb,
treatment = Stim == "SPIKE",
control = Stim == "DMSO",
iterations = 40000)

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 2, 7

As far as I can tell, there is no issue with the metadata or counts. The data structure of the compass container, however, must be causing some issue?

[emjbishop]

Myself and three other people are all getting the same error now when running the COMPASS function, using different datasets (including test data that used to work) and systems (linux, macOS, and windows). Is there a dependency that was updated this year causing this?

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 2, 7

[gfinak]

Can you share data / code so that I might reproduce the error?

[emjbishop]

@gfinak yes, we have a tutorial repo that uses COMPASS. You just need:

• This script: https://github.com/seshadrilab/tutorials/blob/main/flow_analysis_COMPASS/flow_analysis_COMPASS.Rmd
• Example data: https://www.dropbox.com/sh/snr4ycge3jdm50k/AAA4RaV64vDgRXr04wkm9YeMa?e=1&dl=0

Here is a more complete error message with context:

> CC <- COMPASSContainerFromGatingSet(gs,
+                                     node = parent_node,
+                                     individual_id = id,
+                                     mp = markermap,
+                                     countFilterThreshold = 5000)
Extracting cell counts
Fetching 4+
Fetching child nodes
common markers are: 
Time FSC-A FSC-H SSC-A CD8b TNFa CD107a CD154 CD3 IL2 CD4 IL17a IL4_5_13 CD14_19 CCR7 CD38 LD IFNg CD45RA HLADR 
Extracting single cell data for 4+/IL2|4+/IL4513|4+/IFNG|4+/TNF|4+/IL17|4+/154|4+/107a
..............................Creating COMPASS Container
Filtering low counts
Filtering 0 samples due to low counts
Warning message:
In COMPASSContainer(data = sc_data, counts = counts, meta = pd,  :
  There appear to be negative intensities in the 'data' supplied.
> fit <- COMPASS(CC,
+                treatment = STIM == "Spike 1",
+                control = STIM == "DMSO",
+                iterations = 100)
There are a total of 5 samples from 5 individuals in the 'treatment' group.
There are a total of 5 samples from 5 individuals in the 'control' group.
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 2, 7

I've also heard from a colleague (edit: @quinnpeters) that they don't get the error with a much older version of R (v3.6.3).