Question: Expression Matrix And Pearson'S Correlation Coefficient
0
gravatar for pixie@bioinfo
6.0 years ago by
pixie@bioinfo1.4k
pixie@bioinfo1.4k wrote:

I have an expression matrix : Gene ids on 1st column followed by the expression values across control(first 3 ) and disease samples(last 3)

4325938 202.27 312.55 245.61 1.86 55.45 31.71
4330851 181.01 406.12 272.17 73.65 155.02 108.06
...etc

I want to code for finding the correlation values between the genes using Pearson correlation using numpy or scipy module in Python as given in the following reference:
stackoverflow

scipy docs

I am not able to understand what is array x and array y here. What should be the parameter that I should pass to the modules in this case ?..do I have to take a row mean of the expression values for each gene and then pass ? Kindly Help..

ADD COMMENTlink modified 6.0 years ago by ff.cc.cc1.3k • written 6.0 years ago by pixie@bioinfo1.4k
1
gravatar for ff.cc.cc
6.0 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

Hi,

for every row of your matrix

  x is the array made of 6 case-control values

  for every row following x

     y is the array made of 6 case-control values

     compute correlation of x and y

     save result

  end loop over y

end loop over x
ADD COMMENTlink written 6.0 years ago by ff.cc.cc1.3k

Thank you so much..it worked fine!

ADD REPLYlink written 6.0 years ago by pixie@bioinfo1.4k

Did you make an R script for this? Do you mind sharing it?

ADD REPLYlink written 3.2 years ago by Palgrave20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1958 users visited in the last hour