train classifier on bulk RNA-seq dataset

[Noah Simons]

Hello, 

I'm interested in using Garnett to classify single-cell data from macaque PBMCs. Using the pre-trained classifier from human PBMCs works well for classifying a few cell types in macaque, but not for others (e.g. NK cells). I don't have cell-type-specific single-cell data from macaque PBMCs to train a new classifier, but I do have flow sorted PBMC cell-specific bulk RNA-seq data from macaques. Would it be possible to train the new classifier with the bulk RNAseq data?

Thanks,

Noah

[Hannah A Pliner]

Hi Noah,

Garnett is not designed to train on bulk RNA-seq data, but you should be able to train on the same data you're trying to classify!

Best,

Hannah

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Health Sciences Building (HSB) H564E

Seattle, WA

206-616-0454

hpl...@uw.edu

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[Noah Simons]

Hi Hannah,

Ok, that's even better then! Thanks very much!

Noah

On Monday, June 10, 2019 at 1:12:02 PM UTC-4, Hannah A Pliner wrote:

Hi Noah,

Garnett is not designed to train on bulk RNA-seq data, but you should be able to train on the same data you're trying to classify!

Best,

Hannah

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Health Sciences Building (HSB) H564E

Seattle, WA

206-616-0454

hpl...@uw.edu

On Mon, Jun 10, 2019 at 9:45 AM Noah Simons <noahd...@gmail.com> wrote:

Hello, 

I'm interested in using Garnett to classify single-cell data from macaque PBMCs. Using the pre-trained classifier from human PBMCs works well for classifying a few cell types in macaque, but not for others (e.g. NK cells). I don't have cell-type-specific single-cell data from macaque PBMCs to train a new classifier, but I do have flow sorted PBMC cell-specific bulk RNA-seq data from macaques. Would it be possible to train the new classifier with the bulk RNAseq data?

Thanks,

Noah

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