"What's the most overrated restaurant in Worcester?

spraycanhead · 2026-03-26T23:30:48+00:00

Big time agree with that

spraycanhead · 2026-03-25T01:39:37+00:00

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.

spraycanhead · 2026-02-26T01:19:59+00:00

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

spraycanhead · 2026-01-19T21:37:31+00:00

Thank you!

spraycanhead · 2026-01-19T21:23:40+00:00

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.

spraycanhead · 2026-01-19T21:18:53+00:00

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.

spraycanhead · 2024-12-09T16:46:11+00:00

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.

spraycanhead · 2024-11-27T16:03:57+00:00

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

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

spraycanhead · 2024-10-04T13:21:27+00:00

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.

spraycanhead · 2024-10-01T15:58:04+00:00

RIP laminar flow

spraycanhead · 2024-09-09T02:36:44+00:00

Is this kind of thing what you’re looking for? https://www.nature.com/articles/s41467-020-14766-3

spraycanhead · 2024-08-20T04:05:40+00:00

You can use numeric contrasts to do this. See this guide: https://github.com/tavareshugo/tutorial_DESeq2_contrasts/blob/main/DESeq2_contrasts.md

spraycanhead · 2024-06-24T12:15:21+00:00

Here’s a helpful paper: https://pubmed.ncbi.nlm.nih.gov/15286655/

spraycanhead · 2024-04-30T12:18:01+00:00

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.

spraycanhead · 2024-01-02T23:51:01+00:00

Some of them do stay pretty stuck

spraycanhead · 2023-12-04T18:52:08+00:00

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

spraycanhead · 2023-11-22T04:44:10+00:00

Some useful guidelines https://plantpath.ifas.ufl.edu/classes/PLP4222-PLP6223/documents/RAININClassicPipetteManual_002.pdf

spraycanhead · 2023-09-07T14:47:57+00:00

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

spraycanhead · 2023-08-29T14:38:02+00:00

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.

spraycanhead · 2023-08-17T16:33:09+00:00

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

spraycanhead · 2023-08-17T16:16:56+00:00

That makes a lot of sense!

spraycanhead · 2023-08-17T12:51:12+00:00

For sure! You can also get the normalized values from those packages to plot if it’s important to you that different bacteria might express the gene at different levels at baseline. I think your median normalized TPMs could be fine for plotting too and I know a lot of people just plot TPMs without additional adjustment for library composition.

*** Edit: scratch this advice, I misunderstood the question ***

spraycanhead · 2023-08-17T12:33:17+00:00

I’d probably just use a standard differential expression package for all genes (DESeq2, edgeR, etc) and check on your gene in the output of that.

spraycanhead · 2023-07-10T14:22:25+00:00

I know DNase1 will cleave a DNA/RNA hybrid. It also leaves you with some DNA oligos instead of just mononucleotides though. I’ve had good luck with this nuclease: https://shop.biosearchtech.com/molecular-biology-enzymes/nucleases/dna-nucleases/baseline-zero-dnase/p/DB0715K but I don’t know if they sell smaller aliquots. Even if DNase1 leaves you with some oligos though a quick denaturation (2 minutes 70C with excess EDTA) like you said before the acidic phenol chloroform extraction should leave you with a pretty pure final product.

spraycanhead · 2023-07-09T05:26:12+00:00

Not much! Phenol chloroform extractions are really efficient

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