Entering edit mode
3.8 years ago
AnnaW
▴
20
Dear All,
I'm trying to identify driver events from CNV data using oncodriveCIS. It's essentially requires a use of Copy number and expression data.
OncodriveCIS is provided with GBM example data and this one works perfectly.
However when I'm doing the analysis with my own data
python oncodrivecis.py \
-e $DATA_PATH/expression.sampleswithSNP.arrays.tsv \
-c $DATA_PATH/CNV.SNP.array.TARGET.NB.and.normals.tsv \
-s $DATA_PATH/samples.to.process.SNP.arrays.tsv \
-o $DATA_PATH/20200723_OncodriveCIS_SNParrays \
-i $DATA_PATH/ensembl63_ensembl2hugo.tsv -p NB
I'm getting this type of an error:
File "oncodrivecis.py", line 59, in oncodriveCIS
amp_eisN_dict, amp_eisT_dict = calculate_eis(options, cnv_dict, '2') File "/gpfs01/home/x/oncodriveCIS/oncodrivecis-1.1.0/src/lib.py", line 171, in calculate_eis
eisN_subdict = get_eis(exp_header_s, normal_positions, tumor_alt_positions, exp_l_s) File "/gpfs01/home/x/oncodriveCIS/oncodrivecis-1.1.0/src/lib.py", line 69, in get_eis
eis = eis_calculation(float(exp_l_s[tumor_alt_position]), ref_median, ref_IQ, tumor_alt_IQ) File "/gpfs01/home/x/oncodriveCIS/oncodrivecis-1.1.0/src/lib.py", line 52, in eis_calculation
eis = (exp_v - ref_median) / (abs(ref_IQ) + abs(tumor_alt_IQ)) ZeroDivisionError: float division by zero
I have checked and I don't have any zeroes in my dataset. I also eliminated genes with low expression levels. Any ideas what I could improve?