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lmweber / diffcyt

R package for differential discovery analyses in high-dimensional cytometry data
MIT License
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Diffcyt for two different columns #49

Open shanh1 opened 1 year ago

shanh1 commented 1 year ago

Hi there,

I am trying to do an analysis for two different columns of data.

Column 1 is Reticulocyte count at T0 and column 2 is Reticulocyte count at T1.

I want to compare patients with "Normal" in T0 to patients with "High" in T1, where the factors for both columns are "Normal", "Low", "High" and "N/A".

In the past, I have just filtered SCE objects to give me patients with desired factors (e.g. "Normal" and "High") and used contrast 0,1 to compare baseline with condition. But I am now interested in comparing across multiple columns.

How can I set up an analysis for this? Is this possible?

Thank you!

markrobinsonuzh commented 1 year ago

HI @shanh1,

Another option is to form a single column from your two columns and use that to identify the experimental conditions, and then form a contrast for the difference of interest.

Cheers, Mark