Re PCAtools and data entry - novice having issues

Question

[j.marchesi]

Hi Guys

new to using PCAtools and have issues getting my data in. I have 2 data files, one is a matrix of features against samples e.g. gene expression data for a sample, and many samples, the other is a csv file of the sample metadata - where the sample came from, the patients disease status etc.

Any ideas how I get the two into PCAtools so I can create clustering and ellipses in PCA biplots etc?

I can get the matrix in, but I can't work out how to get the metadata in so it matches the matrix.

cheers

Julian

Answer 1

[Kevin Blighe]

Hey Julian, I also received your e-mail. Basically, the rownames of the metadata has to equal the colnames of your input data. In your case, I think that you just have to set the rownames of your env object.

I set this strict requirement from the first step in order to ensure that the numerical data is perfectly aligned with the metadata.

Kevin