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License: GNU General Public License v3.0
Discrete Distributional Differential Expression
License: GNU General Public License v3.0
Thanks for making the code accessible! I found a potential bug in the '_readHeader function in D3EUtil.py. The number of columns are enumerated by the number of tabs in the first row but, typically, the row ends with the last label, not a tab, so the second group is always one short of the number of columns in the file unless you insert a tab at the end of the header file.
There seems to be an error in the wiki for making the control file, as well as in the file name for the .py script.
A control file can be created by using makeControl.py which has the following syntax:
python makeControl inputFile outputFile label
Hence in our case we run:
python makeControl example.txt example_control.txt G1
Should be:
python D3EMakeControl.py inputFile outputFile label
And the filename has a typo, it's missing the 'r' in Control.
Thanks!
To be deleted
I have a problem concerning p values in the output table of D3E.
A lot of them are NaN (around 80%).
I run the analysis in this sequence:
D3EMakeContol.py infile infile_ctrl Group1
D3ECmd.py infile infile.out Group1 Group2 -m 1 -t 0 -z 0 -n 0
D3ECmd.py infile_ctrl infile_ctrl.out Group1_1 Group1_2 -m 1 -t 0 -z 0 -n 0
D3EAnalysis.py infile.out infile_ctrl.out outfile 1
I have tried it with t 0
and t 3
.
It is a set of around 10 000 genes so I am running the job in parallel.
I do this by splitting the original table big_infile
:
D3ESplitData.py big_infile Group1 Group2 ./ 300 1
This will create a few smaller tables which are prefixed Group1_Group2_
.
For each of them I run the sequence described above.
Then I merge the resulting outfiles with:
D3EMergeOutput.py ./ final.out Group1 Group2
I noticed D3EMergeOutput.py removes rows -- always the first row after the header.
I think line 37 in D3EMergeOutput.py should be commented out.
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