Closed lgatto closed 4 years ago
Indeed, I was hesitating to do this when writing that note. I would go for the 2nd solution and create a mock assay. What do you think about calling it failed_run
to explicit the procedure?
In the end, I added one of the blank samples available from the SCoPE2 dataset.
readSCP(mqScpData,
sampleAnnotation,
batchCol = "Set",
channelCol = "Channel")
An instance of class QFeatures containing 4 assays:
[1] 190222S_LCA9_X_FP94BM: SingleCellExperiment with 334 rows and 16 columns
[2] 190321S_LCA10_X_FP97_blank_01: SingleCellExperiment with 109 rows and 16 columns
[3] 190321S_LCA10_X_FP97AG: SingleCellExperiment with 433 rows and 16 columns
[4] 190914S_LCB3_X_16plex_Set_21: SingleCellExperiment with 321 rows and 16 columns
So, this new 190321S_LCA10_X_FP97_blank_01
assay is real data
In your example, the filtering doesn't remove any features. Indeed, you mention
I was wondering if you couldn't use either different a value that removes an assay (but only for demonstration and then carry on with all of them), or add a 4th handcrafted low-quality assay with less PSMs that would be filtered out.