Dear Sir,
I have been using the combat module in gene pattern package..I have successfully formatted the files and introduced the preprocessed ones to the modules yet I got this message.
Error in matrix(0, length(vec), nlevels(vec) - start + 1) :
invalid 'ncol' value (< 0)
Calls: parseCmdLine ... gp.combat.R -> ComBat -> design.mat -> build.design -> matrix
Execution halted


How can i fix this and what does it meaan.

I had two other output1- PNG file: black!!!
2- text file showin this content:
Reading Sample Information File
Reading Expression Data File
[1] "APOBEC3B" "APOBEC3C" "BASI/BSG/CD147" "BATF" E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E13 A1 A2 A3 non1 non2 non3
1 20 20 20 20 20 20 20 20 20 20.00 20 20 20 20 20 20 83.00 95.01 54.00
2 20 20 20 20 20 20 20 20 20 72.45 20 20 20 20 20 20 1389.16 1734.13 709.18
non4 non5 non6 non7 non8 non9 O1 B1 O2 B2
1 54.00 55.99 108.99 84.98 144.01 324.93 20.00 20.00 20.00 36.99
2 709.18 1858.60 998.07 750.13 2876.30 2288.20 455.09 905.14 962.74 1038.29
B3 B4 O3 O4 O5 non10 non11 non12 non13 non14
1 20.00 27.00 41.01 20.00 154.02 73.01 79.01 51.98 20.00 148.98
2 586.91 824.29 528.95 570.07 2019.80 633.85 696.99 1234.75 59.01 798.97
Found 2 batches
Found 2 covariate(s)

I would appreciate your help.
Many thanks
Shaymaa