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cozygene / feather

Permutation testing for heritability and set-tests.
GNU General Public License v3.0
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Failed reading phenotypes file #6

Open frucelee opened 3 years ago

frucelee commented 3 years ago

Dear, Thank you for the perfect software. It reported to me that failed reading phenotypes file when I used this software. Traceback (most recent call last): File "./permutation_testing.py", line 455, in phenotypes = loadtxt(args.phenotypes) File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 1146, in loadtxt for x in read_data(_loadtxt_chunksize): File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 997, in read_data items = [conv(val) for (conv, val) in zip(converters, vals)] File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 997, in items = [conv(val) for (conv, val) in zip(converters, vals)] File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 734, in floatconv return float(x) ValueError: could not convert string to float: 'NA'

Was it the problem due to existing of the NA value? However, at some time, there was some missing value in our dataset. Do you know how to deal with it? Best, Lee

regevs commented 3 years ago

Thank you for your interest in the method.

The method cannot (and shouldn't) handle missing values. I recommend removing the missing samples before proceeding.

On Thu, Apr 15, 2021 at 11:25 AM frucelee @.***> wrote:

Dear, Thank you for the perfect software. It reported to me that failed reading phenotypes file when I used this software. Traceback (most recent call last): File "./permutation_testing.py", line 455, in phenotypes = loadtxt(args.phenotypes) File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 1146, in loadtxt for x in read_data(_loadtxt_chunksize): File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 997, in read_data items = [conv(val) for (conv, val) in zip(converters, vals)] File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 997, in items = [conv(val) for (conv, val) in zip(converters, vals)] File "/home/lee/miniconda3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 734, in floatconv return float(x) ValueError: could not convert string to float: 'NA'

Was it the problem due to existing of the NA value? However, at some time, there was some missing value in our dataset. Do you know how to deal with it? Best, Lee

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