Notes

Dec 17th: line=line.split() ->convert a string into a list

Dec 26th:

1. "else" is only connected to the nearest "if".

• e.g.: cleaning_data_stage2.py, csv3

2. Q: The opened file doesn't work in several lines later. Why?
3. Problem recorded: The cleaned up data count has 88 columns, including the TranscriptID column. But it should be 89 columns right??

Dec 27th:

1. 11.11 am->installed pandas successfully.

Dec 28th:

1. Note: You cannot read lines in two different files within the same "for"loop! ***e.g.:

***for line1 in f_atlas: line1=line1.strip().split('\t') #print(line1[2]) for line2 in f_before: if line2[0]==line1[2]: print(line2[0]) Will only print out the lines in f_before once.

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Jan 1st: The number of pathways I got(KEGG, go) is more than Dimitri's result. Haven't figure out why... For now, just use Dimitri's result to do downstream analysis.

Jan 2nd: ***R information when running Piano: ***Error in checkLoadArg(geneLevelStats, directions, geneSetStat, signifMethod, : signifMethod='nullDist' is not allowed for geneSetStat='tailStrength'