Entering edit mode

Pierre Lindenbaum
▴
10

@pierre-lindenbaum-6329
Last seen 7.3 years ago

Hello, I'm trying to run the MEDIPS package with the following script
(loop over each chromosomes, compare each conditions )
everything works fine for the chr1 but at some point, the script
raises
an error for the chr2. (see below).
Does anyone know what I've done wrong here ?
Thank you
Pierre
(...)
Preprocessing MEDIPS SET 6 in MSet2...
Calculating calibration curve...
Performing linear regression...
Intercept: 1.23986548019807
Slope: 1.72956076992792
Calculating relative methylation score...
Estimate methylation...
Differential coverage analysis...
Extracting count windows with at least 1 reads...
Extracting non-zero coupling factor windows...
Execute edgeR for count data of 1524540 windows...
(Neglecting parameter 'type')
Creating a DGEList object...
Apply trimmed mean of M-values (TMM) for library sizes
normalization...
Estimating common dispersion...
Estimating tagwise dispersion...
Calculating differential coverage...
Adjusting p.values for multiple testing...
Please note, log2 ratios are reported as log2(MSet1/MSet2).
Creating results table...
Adding differential coverage results...
Total number of windows: 5701362
Number of windows tested for differential methylation: 1524540
Remaining number of windows with adjusted p.value<=0.1: 0
Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) :
number of columns of matrices must match (see arg 2)
Calls: myMedipAnalysis -> MEDIPS.mergeFrames -> rbind
Execution halted