Question: Re PCAtools and data entry - novice having issues
0
gravatar for j.marchesi
25 days ago by
j.marchesi0
j.marchesi0 wrote:

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

r pcatools • 96 views
ADD COMMENTlink modified 25 days ago by Kevin Blighe63k • written 25 days ago by j.marchesi0
1
gravatar for Kevin Blighe
25 days ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

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

ADD COMMENTlink written 25 days ago by Kevin Blighe63k
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