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IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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error when PlotGeneralQC(em.set) #11

Closed MichaelPeibo closed 6 years ago

MichaelPeibo commented 6 years ago

I had an error when I did raw.qc.plots <- PlotGeneralQC(em.set)

I skipped the 'Adding additional metadata to the EMSet' step, because I did not have the batch info and certain gene I want to see; instead, I directly run

raw.qc.plots <- PlotGeneralQC(em.set)

after get em.set object from

em.set <- NewEMSet(ExpressionMatrix = matrix, GeneInformation = genes, CellInformation = barcodes, Controls = controls)

The error is

Error in [.data.frame(cell.information, , 2)] : undefined column selected

Any suggestion on this?

MichaelPeibo commented 6 years ago

Update same problem when I run the RunDiffExpression(clustered.set, condition.a = "TRUE", condition.b = "FALSE", conditions = "THY1", fitType = "local", method = "per-condition")

There is an error reporting that: Error in $<-.data.frame(*tmp*, TH, value = logical(0)) : replacement has 0 rows, data has 3679

I doubted this is because I skipped the previous thy1 true or false step, could you have any sugguestion for avoiding this? Because I only have one batch and I actually do not need/have that info. Thanks if anyone can help, I am really fresh in R or bioinformatics

MichaelPeibo commented 6 years ago

Update Sorry to bother this, I REALLY miss one important step, which caused me get the error in the later step

asenabouth commented 6 years ago

Great that you managed to get it working. Keep us posted if you run into any additional issues on the issues page, or email me at a.senabouth @ imb.uq.edu.au