Error running aggregateCount

[jonoave]

Hello,

I’m trying tor run the analysis on GeoMx data following the guide here: https://bioconductor.org/packages/3.14/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#

I checked out GitHub and found some replies suggesting to email the support.

I’m having some issues with this particular step at 4.3: Create Gene_level Counts.

# Check how many unique targets the object has
length(unique(featureData(geomx_data_QC)[["TargetName"]]))
#> [1] 19963
geomx_data_QC <- NanoStringGeoMxSet(geomx_data_QC, check=FALSE)

# collapse to targets
target_geomx_data_QC <- aggregateCounts(geomx_data[["exprs"]])

Trying to run aggregateCounts return this error message:

> target_geomx_data_QC <- aggregateCounts(geomx_data_QC)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'args' in selecting a method for function 'do.call': invalid first argument

Some information on the geoMx_data_QC object:

> geomx_data_QC
NanoStringGeoMxSet (storageMode: environment)
assayData: 20174 features, 66 samples 
  element names: exprs, preLocalRemoval, rawZero 
protocolData
  sampleNames: DSP-1001660003273-B-A02.dcc DSP-1001660003273-B-A03.dcc ...
    DSP-1001660003274-B-C01.dcc (66 total)
  varLabels: FileVersion SoftwareVersion ... NegGeoMean (24 total)
  varMetadata: labelDescription
phenoData: none
featureData
  featureNames: RTS0060887 RTS0060888 ... RTS0081637 (20174 total)
  fvarLabels: RTS_ID TargetName ... OutlierFrequency (11 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: Mm_R_NGS_WTA_v1.0.pkc 
signature: none
feature: Probe
analyte: RNA

Packages used:

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Users/junhoe/micromamba/envs/qlriu-geomxtools/lib/libopenblasp-r0.3.27.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] readxl_1.4.3             kableExtra_1.4.0         knitr_1.46               limma_3.58.1            
 [5] patchwork_1.2.0          GeomxTools_3.5.0         NanoStringNCTools_1.10.0 ggplot2_3.5.1           
 [9] S4Vectors_0.40.2         Biobase_2.62.0           BiocGenerics_0.48.1      dplyr_1.1.4

Thanks in advance for any help or suggestions!

[github-actions]

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