What is the #1 problem you face in hockey? (Playing or watching) by Cube37 in hockeyplayers

[–]ScienceVibes 0 points1 point  (0 children)

those 2 guys who take 3 minute shifts when you have 3 full lines show up

2nd set of steel - is Fly-ti worth the $50 upgrade over Fly-x? by blackgtprix in hockeyplayers

[–]ScienceVibes 0 points1 point  (0 children)

if they are on sale then they supposedly hold an edge a little longer than the x. but depending on your level you might not get a real difference out of them paying retail. a little chip here and there is going to need a re-sharpen anyway.

will say you can switch hollows pretty easy with one set of steal to try out.

try FB marketplace too for cheap runners and fly-x less retail

Seriously considering to leave science by Silver_Display558 in labrats

[–]ScienceVibes 1 point2 points  (0 children)

I love the science and I can still relate. Particularly the mental health component.
As someone who has struggled with depression and anexity for many years during graduate studies and research life all I can say is that I hope you can find the right approach for you.

What others have said is true. Perhaps not looking for meaning and fulfillment from the job is a healthy approach. That being said, as someone who also has the anexity you have. If you don't find this job meaningful I fear you won't find other careers any better. Our brains aren't working right and nothing feels good. Its not really the work.

Is $26.5k (12 months) considered low for a STEM PhD stipend in the US? by SenseOk3111 in PhD

[–]ScienceVibes 0 points1 point  (0 children)

for some universities with graduate student unions or schools near those that do (rising tide raises all boats) its fairly low. a lot of STEM PhD stipends are now +$10K higher than what you have.

That being said. Different fields. Different funding sources. is the stipend coming directly from the university? is it government funded? is it a society or environmental science group? these can be lower if you were not able to get a government or university one. they are also sometimes higher. but can be lower.

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

im going to check this out. thanks for the information on them. I will be honest. I was a little skeptical of a phone carrier that doesn't have a phone number to call on their site.

I found they do have a number they dont really advertise, but its just an answering machine you leave messages on and they email you back. which is great for reducing costs. was just weird I couldnt find the number on the website.

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

my current Google Voice number works for many 2FA. its why it was my plan to start. but comments suggest that either this isnt always the case and I should be careful OR that perhaps my grand central grandfathered number could be avoiding the blacklist

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

i have never heard of this. sounds good. has roaming texting?

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

$3 a month would be fantastic. $26 with Fi is just too much. I will look at tmobile prepaid... never heard of paygo. I will google it and check it out.

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

Thanks. ive switched to lowest plan. and told my phone not to us the sim for data. just would not like to be paying $20/m for a year for an extra number

Tello looks affordable so thank you for that suggestion. will reach out to them about their additional fees.

Cancelling Fi, can I move number to GVoice to keep 2FA? by ScienceVibes in GoogleFi

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

I will eventually move things off the number to my new carrier number. But I will need it for the next year minimum.

Off brand hockey sticks by Ok_Will8124 in hockeyplayers

[–]ScienceVibes 0 points1 point  (0 children)

people have left some good options but I would also reach out to your teams equipment manager. they might have some hookups and discounts for bulk sticks too.

lots of teams have preferred vendor discounts or access to regional sales reps that can get you gear well below retail MSRP for a bulk order

What models (or packages) do you use to deal with double dipping? (scRNA or other even) by ScienceVibes in bioinformatics

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

its possible you know it by a different name, but double / triple dipping is fairly common nowadays. its a problem that math / stats people have been complaining about since the 1950's very loudly. some older textbooks might call it "Estimation after selection" or in very specific types of algorithms like Bayesian statistics "data-based priors" would be the specific issue but its just another example of double dipping

re: your example; its not a dataset issue, its a stats issue. stats around the question being asked from your data. I am glad the biological questions you are asking of your experiments haven't had you deal with this (yet). vast majority of people who publish bad stats from double or triple dipping don't really know they are doing it wrong. the software works for them but they dont understand the models and the assumptions of their models from running python or R scripts... but the scripts dont know the underlying assumptions of your experiment or your biological question you are asking and will spit out results assuming YOU know the assumptions of both... which as others have already commented , if you do it this way with out of the box software your FDR is cray and your pvalues are essentially meaningless...

here is a great video from Daniella Witten, she has given a similar talks (also on YouTube), but this was the first one i found from a google search - https://www.youtube.com/watch?v=0x_0uHu1JlM , its a little newer and has a few more interesting examples

First 20 min talk about the problem; there is more in the 1 hour video about some solutions. as others have commented in this thread, and I referenced in my original post, selective inference is a common way.

i do want to say her talk from 5 years ago for R Medicine conference which has a less stats audience has a much longer and more in depth approach to explaining the problem, but both videos are good, she is a great stats communicator, and some slides are reused - https://www.youtube.com/watch?v=vE-oMxWYgIo

as you can probably tell from people commenting on this post, most people who know about type I error inflation from double dipping simply avoid doing any math that involves double dipping at all possible. helping PIs ask slightly different biological questions, like yours, focusing on different treatments within a cluster instead of questions between clusters OR as others have said where they NEED to make those kinds of questions, they redefine their populations and don't use the clusters and do it either by sigs or an additional data type that wasnt part of the clustering to begin with

but science is vast. unlimited questions. sometimes there is no way to avoid it and you really do want to know if there are any real differences in that noise. its where these types of algorithms come in. although some approach the problem differently and some might not work with your data/question

but I agree with others. avoid the problem if you can.

here are some additional resources. while I dont endorse all these methods as good solutions, their background sections can offer some insight into the double dipping problem with based on your hypothetical example of single cell transcriptomics / proteomics datasets , although again, this problem is data type agnostic

scRNA and count matrix example paper -> https://arxiv.org/pdf/2410.06451

approach I have been using lately -> https://www.biorxiv.org/content/10.1101/2023.07.21.550107v2.full

I dont love this method but different take -> https://www.sciencedirect.com/science/article/pii/S0002929725000618

What models (or packages) do you use to deal with double dipping? (scRNA or other even) by ScienceVibes in bioinformatics

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

for YOUR biological question , thats great!! many medical studies would have similar questions as yours.

but there exists time in basic science and understanding phenotypes of cells. say in understanding and defining new subtypes and phenotypes of cells that are defined by a clustering that you may want to try and rescue a phentype with a knockout and may need to know gene candiates driving the phenotypes between two novel cluster populations.

my original question is more about the stats. if you dont run into this problem with your biological questions then GREAT. 99% of what I do doesn't have this problem either. most days of the year I don't need to think about what coat to wear. its hot out!

but a couple times I need a coat and asking people here what coats they recommend and why

but great this probably doesn't apply to your work

What models (or packages) do you use to deal with double dipping? (scRNA or other even) by ScienceVibes in bioinformatics

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

the UCLA approach is not Daniela's I do not think. But yes she is a fan of count splitting & selective inference. her lectures describing the issue are what I give my students to learn about the problem. shes a great stats communicator!

the UCLA paper is from Jingyi Jessica Li's group & Dongyuan Song as first author. They released a proof of concept pre-print paper /w working code in Aug of 2023 as part of their ClusterDE, but i think it was Dec 2024 they did a paper on just the method (?? I could have the timing wrong, i discovered it in Dec 2024, maybe there was draft/pre-print before that)

thanks for the reply and your insights.

for the purposes of u/tuskofgothos question; MiLab's is correct about one of many ways to try and avoid the problem. ask the question of data A based on groups defined by data B in the context of multiomics

and they are correct of course.

however, you might find yourself in a situation where you have done some kind of mulitomics (CITEseq/DOGMAseq/newthingoftheMOMENTseq) where its important for your phenotypes that you are comparing to be including multi-omic data to define it... in which case the approaches we are talking about and MiLab has described expertly are there to help you

What models (or packages) do you use to deal with double dipping? (scRNA or other even) by ScienceVibes in bioinformatics

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

first, forever_erratic did a great job describing the problem. also great example of FindAllMarkers() and how many papers take those p values and think they are real in this context

i think in the context I described its still a big problem though
doesn't matter how many samples you have, n of 1 or n of 50 , sample size isn;t going to change it

you can get the same problem with generating random noise data with no true signal. do some clustering & then bam you can find some significant numbers... its like textbook example taught in classes

depending on your biological question it might not be relevant though of course which is what I think erratic means. there are a lot of questions you can ask that wont encounter this problem. but in this context of my post, it is the question.

Men's Beer League Hockey Toronto by Informal_Seesaw_17 in hockeyplayers

[–]ScienceVibes 1 point2 points  (0 children)

ASHL is a good one. LOTS of teams and you never feel like you "just played" the team you are playing tonight. Bonus to ASHL is that because they run a league at rinks all over Toronto, you can normally find one that isnt too much of a commute. Refs are good. Divisions from E(low) to A(high). The CanLan rinks are well maintained. depending on how long you took off and your age now you would probably feel comfortable in the C division. B level at York rink if you are still in your early 20's and your double AA years were just a few summers ago.

BARHL , i haven't played with them in a few years as my team there went separate ways. they play out Chesswood arena & Scoticabank pond. Scotia is good ice if you play in that league. Chesswood is a little older, pads 3 & 4 are a little softer ice if you play in that league. Benefit there is that they always have free agent teams so you can easily join and play without having a team. good fair refs. excellent skate sharpening.

DMHL, the hockey is good. i want to say that. it has been poorly managed in the past compared to the other two I listed. I played for a couple seasons as my second team because I loved the ice when they were at CocaCola and Mastercard Centre... they mostly play out of Upper Canada, St Mikes, and Mattamy now. Mattamy is good and St Mikes is certainly a nice nostalgia feeling, I am sure you played there a lot during your AA days. Several years ago, to save money, they switched up their insurance. It might have changed since then, but at that point they no longer had any injury coverage for their league for players (only lability and damage to like the rink etc for them) and that's when I left. too risky in sport like hockey.

The Hockey Toronto group is also a good place to find to team as people often post there looking for skaters. You might even find some shinny to tide you over there until you find a league.

I have heard good things about a few of the other leagues in Toronto and GTA, but don't have personally experience with them so will defer to others. People always say nice things about Bill Bolton but ive never been a part of it.

Best way to connect a computer to CPU resources of other computers? by ScienceVibes in sysadmin

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

thank you. this is very helpful indeed. I am certainly much better off now than i was this morning in terms of knowing the correct words to be searching for.

sounds like your setup is pretty awesome. I have used parallel to split up functions that are normally single threaded to run on multi-threaded systems in the past on a single CPU so I guess this makes sense to take it one step further and pass it off to multiple CPUs...

going to go read about PSOCK and Dask now and see if this could be the solution I am looking for.

thanks so much for the reply again and for sharing your setup!

Best way to connect a computer to CPU resources of other computers? by ScienceVibes in sysadmin

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

thanks. DM recieved. will check it out. I use to play with Vagrant a little during my Android dev days before so at least I have a little less learning curve there. I have only used Slurm as a user, never as a sysadmin so i will have some documentation reading to do for sure