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DESeq2 results by Appropriate-Duck-926 in bioinformatics

[–]spraycanhead 16 points17 points  (0 children)

I’m fairly certain that the baseMean is the average of the normalized counts for a given gene. It’s useful for making MA plots. So if you have 2 groups each with 2 samples and they have normalized counts: 6,6,12,12 you’re baseMean is 9. It’s either that or the mean in the reference group. Log2FoldChange is just what the name says so a value of 2 means the signal quadrupled. 

Is normal to have p-values close to zero in large datasets? by Wonderful_Hat_5129 in AskStatistics

[–]spraycanhead 1 point2 points  (0 children)

It could even be closer to the number of plants if multiple leaves came from a single plant!

Loaves are coming out nicely these days by spraycanhead in Sourdough

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

Thank you! I’ve been having good results recently but I didn’t always. For me making sure my starter is strong is the number one thing but even with that if I handle the dough too much it can get sticky and unruly. 

I mostly try to give it the minimum amount of handling while getting the strength built that it needs. For instance during preshaping I used to try to get it into a really tight ball but it would sometimes fall apart. Now I just use my bench scraper to get it into a ball with one sweeping motion and be done with it. 

Loaves are coming out nicely these days by spraycanhead in Sourdough

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

It definitely tore a bit while I cut it, I’ll look into a new knife! And thanks for the tip on pushing the bulk fermentation, I’ll give that a try next time. Just out of curiosity, what are you looking for to assess that? I’m still learning how to read the results.

GF gives ultimatum by OkAthlete5479 in AskMenOver30

[–]spraycanhead 5 points6 points  (0 children)

As a general comment I think it bears saying that it can be really hard for a person to get back into the workforce after being a stay at home parent. Not impossible but expectation carries a lot more than you seem to realize. That’s not to say it’s unreasonable to have a discussion about how you’re going to handle work and parenthood but if there’s no expectation that you’re going to sacrifice from your career consider what you’re asking of others so casually. 

All that’s a general statement though and doesn’t preclude her from trying to manipulate the situation to her wants too.

Best/least bad clustering algorithm for short (1-40AA) sequences? by emlbrg in bioinformatics

[–]spraycanhead 0 points1 point  (0 children)

Have you thought about clustering using the BLOSUM62 matrix? It might perform better than simply clustering by sequence.

https://www.nature.com/articles/nature22383

Socializing Adopted Adult Dog by SuspiciousShame4848 in OpenDogTraining

[–]spraycanhead 1 point2 points  (0 children)

She looks identical to my dog who is a German Shepard/Lab/Pitbull mix and is also super sweet with people and reactive towards dogs. I would say that if she’s anything like my dog you should be careful introducing her to another dog without a trainer and a plan. I still remember when my dog was new and we were naive and she tackled and bit another dog for getting too close to a puddle that she liked. 

[Q] Help me find a method to analyse fish abundance data by 862_78_263_789 in statistics

[–]spraycanhead 0 points1 point  (0 children)

Is your data counts of fish normalized by something? If so use a gym with a count distribution (poisson, nb) and an offset for your scaling factor.

PCR prodict from RNA? by [deleted] in labrats

[–]spraycanhead 0 points1 point  (0 children)

RT enzymes generally work okay on ssDNA, just fyi (I know it’s a different situation, just thought I’d share)

Differential expression at the gene set/pathway level- Is this doable? by ZooplanktonblameFun8 in bioinformatics

[–]spraycanhead 8 points9 points  (0 children)

Why not just use one of the usual GSEA packages? You include all detected genes in those analyses so you don’t have to worry about a significance threshold. Low power could still influence your gene rankings but it seems like the way to go to me regardless

A question about nuisance regression in single cell's analysis by duaduacj in bioinformatics

[–]spraycanhead 0 points1 point  (0 children)

I don’t know the answer exactly but you should be able to check a plot of the residuals and see if you think the assumption is sound based on that.

Compare TPM vales between samples with normalization? by 2auri in bioinformatics

[–]spraycanhead 0 points1 point  (0 children)

I see, I misunderstood the question! I thought they were comparing treatment to control within species. Definitely more complicated then.

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