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.