what to do after pseudotime analysis by Monocle?
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22 months ago
hsu ▴ 40

Hi, I have analysed my data by Monocle and I have constructed pseudotime trajectory. And I try to find genes that change as a function of pesudotime. But the change of expression levels of top genes is not obvicus. How should I do next to find genes which are differntially expressed along the trajectory?

Thank you !

monocle pseudotime • 1.9k views
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22 months ago

The answer is right here: Differential Expression Analysis.

Scroll down to the section entitled 'Finding Genes that Change as a Function of Pseudotime'.

If you have tried this already, then there are many possibilities:

  • there genuinely are no differences along the trajectory for your 'top' genes (and you should neither forcefully try to find differences if they do not exist)
  • your experimental set-up is incorrect / introduces too much bias
  • et cetera

Kevin

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There are not significant differences along my trajectory. What should I do about it?

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If that is the result, then report that as the result. I mentioned other suggestions in my answer, too. Please review each step in your analysis in order to ensure that you have done everything correctly. Also, confirm with the wet laboratory personnel that they have done everything correctly. If you want, let us know the experimental setup (you have not provided it), so that we can provide commentary on it.

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16 months ago
kanwarjag ★ 1.1k

Though it is an old discussion but I want to add to this discussion my problem- I have performed analysis on single cell RNA-seq data of two samples one is disease vs matched control. IN the diseased sample I want to study the lineage analysis to find out how cells have developed into diseased cells, in other words to find out the progenitors of diseased cells. When one does pseudotime trajectories you can assign one as starting cells and map other cells. IN case you don’t have any knowledge which cells are originating cells then how you find out the cell lineage hierarchy. Is there a method. I have tried Monocol, slingshot etc and could not find any straight answer from the instructions.

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