Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Statistical testing for non parametric data
0
gravatar for SOneil
2.1 years ago by
SOneil • 40
SOneil • 40 wrote:

Hi all,

Is there a way to conduct a Kruskal Wallis test or Mann Whitney U on Galaxy Main?

Thank you for your help.
statistics galaxy • 642 views
ADD COMMENT • link •
modified 2.1 years ago by Devon Ryan • 1.9k • written 2.1 years ago by SOneil • 40
3
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Your best bet is the jupyter interactive environment. With the python kernel you can:

from scipy.stats import mannwhitneyu

and then use the mannwhitneyu() function.
ADD COMMENT • link written 2.1 years ago by Devon Ryan • 1.9k

Thank you for you reply, I have been doing that thus far. Although I am not that experienced in python, but is it possible to create a loop that could read certain datasets from the history and carry out testing in that manner ?

ADD REPLY • link written 2.1 years ago by SOneil • 40
2

Certainly! If you post the first few lines of such a dataset I'll show you the appropriate code.

ADD REPLY • link written 2.1 years ago by Devon Ryan • 1.9k

Help via Interactive Environments and Devon, how awesome is this!

ADD REPLY • link written 2.1 years ago by Bjoern Gruening ♦ 5.1k
1

Something like this should work:

datasets = [2,3,4,5,6] # the dataset numbers of your history    
for data in datasets:
    data = get(data)
    for row in open(data):
         columns = row.split()
         print( mannwhitneyu( columns[] ) ) # here you need to access the columns you want to use
ADD REPLY • link written 2.1 years ago by Bjoern Gruening ♦ 5.1k

This is perfect, thank you so much !

ADD REPLY • link written 2.1 years ago by SOneil • 40
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour