Troubleshooting¶
Pickling error¶
Problem¶
When running reademption (e.g. with Python 3.2) you get an error like this:
Traceback (most recent call last):
File "/usr/lib/python3.2/multiprocessing/queues.py", line 272, in _feed
send(obj)
_pickle.PicklingError: Can't pickle <class 'method'>: attribute lookup builtins.method failed
Solution¶
Switch to Python 3.3 or higher. The newer versions can handle this.
DESeq2 unused argument error¶
Problem¶
Whenn running deseq
you get an error similar to this:
Error in results(dds, contrast = c("condition", "XXX", "YYY")) :
unused argument (contrast = c("condition", "XXX", "YYY"))
Execution halted
Apparently DESeq did not generate the file "deseq_comp_XXX_vs_YYY.csv". Extension stopped.
Solution¶
Get a newer version of DESeq2. Version 1.2.10 and higher should work.