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Description
While trying to run this code:
from pyaffy import rma
from collections import OrderedDict
from os import listdir
from os.path import isfile, join
my_cel_files = [f for f in listdir('GSE14245_RAW') if isfile(join('GSE14245_RAW', f))]
sample_cel_files = OrderedDict([
('Sample %d' % (i+1), 'GSE14245_RAW/'+path) for i, path in enumerate(my_cel_files)
])
cdf_file = 'HG-U133_Plus_2.cdf'
genes, samples, X = rma(cdf_file, sample_cel_files)
I got the following error message:
Traceback (most recent call last):
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1741, in
main()
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1735, in main
globals = debugger.run(setup['file'], None, None, is_module)
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1135, in run
pydev_imports.execfile(file, globals, locals) # execute the script
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/gihad/PycharmProjects/cancerproject/data.py", line 13, in
genes, samples, X = rma(cdf_file, sample_cel_files)
File "/home/gihad/PycharmProjects/cancerproject/venv/lib/python3.6/site-packages/pyaffy/process.py", line 118, in rma
parse_cdf(cdf_file, probe_type=probe_type)
File "pyaffy/cdfparser.pyx", line 193, in pyaffy.cdfparser.parse_cdf
AssertionError