Tagged Questions

1
vote
3answers
114 views

How to find genes associated with PC1 and PC2 after the PCA on microarray?

I have run a PCA on my microarray data and found the clustering pattern for my samples. Now I need to find out the genes which are associated with first principal component and likewise till 4th PC. ...
1
vote
1answer
43 views

How do you determine the effect of a simple predictor variable after a PLS analysis?

So, I am running PLS on a genetic dataset with phenotypic and genotypic information. I have about 1000 binary predictors (X), representing molecular markers, for each individual. My indicator ...
4
votes
2answers
284 views

Appropriateness of PCA to visualize clusters in genetic data

I've seen PCA improperly applied in genetic research quite often. I wanted to clarify : when is it appropriate to use PCA as a visualization tool in your analysis? Some examples: 1) Rarely is the % ...
2
votes
2answers
416 views

Mahalanobis distance when n>p

I have an n by p matrix, where n is genes and p is patients. Anyone whose worked with such data knows that n is always larger than p. Using feature selection I have gotten n down to a more reasonable ...
4
votes
1answer
2k views

In genome wide association studies, what are principal components?

In genome wide association studies: What are the Principal Components Why are they used? How are they calculated? Can genome wide association studies be done without Principal Components? Are there ...
2
votes
1answer
674 views

Variation in PCA weights

I have weights of SNP variation (output through Eigenstrat program) for each SNP for the three main PCs. I wish to reduce my list of SNPs to those that show maximum differentiation between the three ...