Question: Restricted Permutations between 4 groups with 2 replicates each
gravatar for manali.rupji
3.2 years ago by
United States
manali.rupji0 wrote:

Hi All,

I am trying to compare 4 groups with 2 samples each (replicates) to understand the differences among each group for a set of 10,000+ genes from a micro array project. I am using the method of permutations and calculating an F statistic as the sample size is too small for a standard t test.

Using an F-statistic and a null of no mean difference, I was able to calculate the obs F- value for each gene in R. But when doing permutations, I understand that there will be 8C2 * 6C2 * 4C2 *2C2 different pairwise permutations which need to be accounted for. I am unable to code for these 2520 permutations in R.

Is there a package that I could look for in R or SAS macro that would help me accomplish the EXACT ORDER of the permutations? I tried the allPerms function from the 'permute' package and the permn function from the 'cominat' package but I am not getting the restricted permutations of interest.

Eg. for 2 group (G1 and G2) setting with 2 replicates each (S1, S2 and S3 , S4): G1 G2 S1 S2 S3 S4 P1: S1 S2 S3 S4 P2: S1 S3 S2 S4 P3: S1 S4 S2 S3 P4: S2 S3 S1 S4 P5: S2 S4 S1 S3 P6: S3 S4 S1 S2

I want to get the exact order of permutations in a 4 group with 2 samples each setting.


ADD COMMENTlink modified 3.2 years ago by ariesliu32420 • written 3.2 years ago by manali.rupji0
gravatar for ariesliu324
3.2 years ago by
United Kingdom
ariesliu32420 wrote:

I have a similar question. Have you found an answer?

ADD COMMENTlink written 3.2 years ago by ariesliu32420
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1685 users visited in the last hour