PCASigGenes crashes if PCA count is higher than the number available about seurat HOT 3 CLOSED

You can look at the number of columns in the rotation matrix.

ncol([email protected])

Based on the JackStraw error message, it looks like you have 4 PCs.

from seurat.

Thanks!

suggestion: when people run your tutorial with a different input matrix, it will fail at this step, because there are not enough PCs. The error message though doesn't make this clear at all. You could catch this error and print something or take the minimum of the current PC count and the supplied number of PCs instead of taking the supplied number of PCs at face value.

from seurat.

Yep, definitely a good idea. We will add this in a future update (or feel free to submit a pull request).

Also, it looks like you're still using the old tutorial. Check out the website for a newer version (http://satijalab.org/seurat/pbmc-tutorial.html)

from seurat.