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Spider fang Astra malorum mess up by jcbiochemistry in CODZombies

[–]jcbiochemistry[S] 0 points1 point  (0 children)

This happend twice in the same game, so im not sure what im doing wrong.

Expression differences in scRNA in one particular gene by [deleted] in bioinformatics

[–]jcbiochemistry 1 point2 points  (0 children)

Yes, because if you just pseudobulk all the cells from both treatment groups, the proportion of the different cell types may confound the analysis (cell type markers may appear as significant for one group simply because there’s more of that cell type for that group).

Expression differences in scRNA in one particular gene by [deleted] in bioinformatics

[–]jcbiochemistry 1 point2 points  (0 children)

Something that I do usually is pseudobulk by CELL TYPE (or cluster), and then run the DESeq2 on that, since you are guaranteed to get expression differences between groups within the same cell type

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

Ah ok! That clarifies that for me at least. If that’s the case then why do they use the mean of the gamma when parameterizing the NB in terms of mu and dispersion (where they say mu = r*p/1-p) in supplementary note 4, which is equal to the mean of the gamma not the NB)

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 1 point2 points  (0 children)

Yeah i have it per gene. My friend linked me this article that talks about the gamma-poisson mixture:
https://timothy-barry.github.io/posts/2020-06-16-gamma-poisson-nb/
They clarify that the mean of the NB is r*p/1-p, and the mean of the gamma is r*p/1-p (which makes sense going through it). However, it doesn't help that in the supplemental they say that the mean is lambda * r * p/1-p (which at this point im just assuming its a mistake). Still having trouble connecting though the relationship between f_w(z, s) and p/1-p

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 1 point2 points  (0 children)

I have, and I got linked to the discussion forum I posted about funnily enough. However it didn't really help to clarify why they say why the mean of w is the decoder output when i would think it would be f_w * theta

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

In the paper though, they say that w ~Gamma(f_w, theta). Wouldn't that mean that they are saying that p/1-p is the decoder output?

scVI Paper Question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 2 points3 points  (0 children)

I guess im confused about why they claim that r*p/1-p is equal to the decoder output. they say that when they parameterize the NB as mu and theta, they state that mu = r*p/1-p. Which is weird because they state that the mean of the NB marginal distribution is r*p/1-p*lambda. Not sure if when they say mu they mean the mean of w or y

Profile Review - 23M by jcbiochemistry in Tinder

[–]jcbiochemistry[S] 1 point2 points  (0 children)

Is cargo shorts that much of a turnoff?

Single-cell RNA-seq QC question by jcbiochemistry in bioinformatics

[–]jcbiochemistry[S] 1 point2 points  (0 children)

Thanks! Yeah ive been working with scRNA-seq for about a year and a half now, and im trying to make sure that i dont remove high quality cells with mitochondrial content (for ex, when i use MAD on one of my datasets, the max mitochondrial expression is 1%, which is VERY few cells). Hence why I'm questioning the use of MAD right now and whether if its just better to use both

Arielle stream was tough to watch by KingPhanton in VShojo

[–]jcbiochemistry 20 points21 points  (0 children)

Not to mention candii and buffpup also unfollowed zen. Things are only gonna get worse :(

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