RCC files not read properly for NanoString PlexSet data
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mcanouil commented
When reading Plexset RCC files which include 8 samples named Endogenous*s
with *
from 1
to 8
.
The Code_Summary
column is not unnested properly, i.e., a two-level list-column instead of a simple list-column.
library(NACHO)
.data <- summarise(
data_directory = paste(params[["data_directory"]], "RCC", sep = "/"),
ssheet_csv = paste(output_directory, "sample_sheet.csv", sep = "/"),
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
)
# > Error in `[[<-.data.frame`(`*tmp*`, "CodeClass", value = character(0)) : replacement has 0 rows, data has 5760
This issue might araise other issues later for normalisation and visualisation.