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SONGDONGYUAN1994 / ClusterDE

A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping
https://songdongyuan1994.github.io/ClusterDE/
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If my goal is just to compare DE between 2 clusters, should the my null dataset consists of all clusters or just the 2 clusters? #4

Open klai001 opened 5 months ago

klai001 commented 5 months ago

Hi dongyuan thanks for the useful package. I have a question because im not sure how to set up the expression mat for constructNull()

If my goal is just to compare DE between 2 clusters, should the my null dataset consists of all clusters or just the 2 clusters?

Also, can call_DE() return a statistic which is similar to LFC since im just comparing the 2 clusters? i would require a signed statistic for the DE gene ranking for a subsequent process.

thank you

SONGDONGYUAN1994 commented 5 months ago

Hi Klai, Your null data should just contain the two clusters that you would like to compare. The output will include a table; inside the table, the cs (contrast score) should be your DE rank. Please let me know if it works for you, thanks!

Best, Dongyuan