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hms-dbmi / scde

R package for analyzing single-cell RNA-seq data
http://pklab.med.harvard.edu/scde
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cde.error.models in batch #62

Open ghost opened 6 years ago

ghost commented 6 years ago

Do you think in scde.error.models you should also take batch effect into consideration?

JEFworks commented 6 years ago

Yes, if you have batch information, you can provide that into the groups parameter so that error-modeling is done in a batch-specific manner.

Jean Fan, PhD Bioinformatics and Integrative Genomics NCI F99/K00 Post-Doctoral Fellow Zhuang Lab | Harvard University 12 Oxford St, Naito 031, Cambridge, MA 02138 web: jef.workshttp://jefworks.com/

On Mar 3, 2018, at 8:52 AM, Poorya Parvizi notifications@github.com<mailto:notifications@github.com> wrote:

Do you think in scde.error.models you should also take batch effect into consideration?

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ghost commented 6 years ago

But the problem is, my single cells have two conditions which both exist in different batches. Do you mean in this case I should have 4 groups?