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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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issues of multi-conditions #101

Closed jsxlei closed 5 years ago

jsxlei commented 5 years ago

e.g. When I run conditions contain A, B, C, I found the summary only had B, C referenced on A, and A had no results, how to calculate all conditions?

gfinak commented 5 years ago

Can you post a reprex, or we can't help you otherwise.

jsxlei commented 5 years ago

according to the tutorial, I got this:

primerid conditionStim cngeneson

100462981 -6.4* 1.5

152926 6.2* -2.9

253512 3.2 -4.6*

26054 4.1 -4.6*

3458 7.3* 0.5

3727 -6.7* 0.5

514 3.1 -4.2*

6482 4.5 -6.4*

but, I want DE of conditionUnstim at the same time, if I have multi conditions, I want them compare each other, not limited to referenced on the same condition.

amcdavid commented 5 years ago

Per the README would be been best directed to the bioconductor support site:: https://support.bioconductor.org/, since this not a bug report. Do either of https://support.bioconductor.org/p/100396/ or https://support.bioconductor.org/p/98420/ answer your question?

gfinak commented 5 years ago

Use the hypothesis argument and set the contrasts you want to test (which is all of them in your case). This is in the manual and at the links Dr. McDavid posted.

jsxlei commented 5 years ago

I got it, Thanks.