# PCA changes: no longer produces files, new --arrays option

**URL:** <https://discuss.hail.is/t/pca-changes-no-longer-produces-files-new-arrays-option/53>\
**Category:** Updates\
**Created:** [October 13, 2016, 6:29pm UTC](https://discuss.hail.is/t/pca-changes-no-longer-produces-files-new-arrays-option/53 "2016-10-13T18:29:21Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [October 13, 2016, 6:29pm UTC](https://discuss.hail.is/t/pca-changes-no-longer-produces-files-new-arrays-option/53/1 "2016-10-13T18:29:21Z")

</div>

PCA writes to annotations instead of files.

1. `--scores [-s]` option is required, defines sa path for the _k_ sample PC scores
2. `--loadings [-l]` option is optional, defines va path for variant loadings (if this argument is not passed, pca will be a little faster)
3. `--eigenvalues [-e]` option is optional, defines global path for the _k_ eigenvalues

The `--arrays` option produces `Array[Double]` for scores and loadings rather `Struct{ PC1: Double, PC2: Double, PC3: Double, ...}`

[https://hail.is/commands.html#pca](https://hail.is/commands.html#pca)