Error running aggregateCount #198
Description
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!