Error report: beta score normalization by positive control
In addition to the problem of negative count value, I met one more problem when trying to normalize the beta score by positive controls.
Using MAGeCKFlute version 1.4.2, I tried 2 ways for positive normalization
- FluteMLE(beta.file,control.cell,treat.cell,posControl =pos.gene,outdir=paste("../graph/FluteMLE"))
- NormalizeBeta(ReadBeta(beta.file),posControl = pos.gene)
But they all showed errors. The beta score summary file is attached.
pos gene:
CDK1
CDK9
PCNA
POLR2A
POLR2D
PRL9
RPA3
RPL23A
Many thanks for your help!
- Error of FluteMLE
2019-07-24 18:10:45 # Create output dir and pdf file...
2019-07-24 18:10:53 # Read gene summary file ...
2019-07-24 18:11:01 # Normalize beta scores ...
2019-07-24 18:11:01 # Violin plot for Negative control normalized Beta Score ...
2019-07-24 18:11:02 # Density plot for Negative control normalized Beta Score ...
2019-07-24 18:11:02 # Density plot for Negative control normalized treat-control beta scores...
2019-07-24 18:11:03 # Violin plot for Cell cycle normalized Beta Score ...
2019-07-24 18:11:03 # Density plot for Cell cycle normalized Beta Score ...
2019-07-24 18:11:04 # Density plot for Cell cycle normalized treat-control beta scores...
2019-07-24 18:11:06 # MAplot for Negative control normalized beta scores ...
2019-07-24 18:11:06 # MAplot for Cell cycle normalized beta scores ...
Error in sum(posControl) : invalid 'type' (character) of argument
In addition: Warning message:
No positive control genes provided !!!
2. Error of NormalizeBeta
2019-07-24 18:11:08 # Normalize beta scores ...
2019-07-24 18:11:08 # Read gene summary file ...
Error in mid - 0.2 : non-numeric argument to binary operator
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