Question

DESingle, Differential expression in single cell rna seq (scRNA)

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bioinfo.himanshu • 0

@bioinfohimanshu-17204

Last seen 5.6 years ago

Hi,

In the manual you have mentioned the differential expression as following:

DEs refers to ***“different expression status”***. It is the type of genes that show significant difference in the proportion of real zeros in the two groups, but do not have significant difference in the other cells.

My doubts is, what other cells (but do not have significant difference in the other cells)? Are you taking into consideration the whole data set not just group 1 and group 2 in TestData? If so then you have only 150 samples in the TestData, how do you compare with other samples? (please correct me if I understood wrong). Could you give more insights into the "other cells" part?

Thank you,

Himan

DEsingle different expression status • 913 views

ADD COMMENT • link updated 5.6 years ago by miaoz13 ▴ 10 • written 5.6 years ago by bioinfo.himanshu • 0

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Sorry my bad! got the explanation! :)

ADD REPLY • link 5.6 years ago bioinfo.himanshu • 0

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Hi, Himan,

Sorry to reply late. Good to see that you have got the explanation for the question, while I also want to psot an answer here in order to help others who have the same question. If you have more questions, please don't hesitate to leave me a message, thank you!

ADD REPLY • link 5.6 years ago miaoz13 ▴ 10

score 0 · Answer 1 · 2018-09-21

Actually, there are no "other samples/cells" except the input to DEsingle. The DEs genes means that, for cell group 1 and group 2 you're comparing, only the "real zeros" proportions of the two groups are significantly different. "The other cells" refers to the other cells in the two group except for the cells which have "real-zero-expression" for this gene. I hope this could help you, thanks.