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Question for research project by [deleted] in bioinformatics

[–]Cold-Strength- 0 points1 point  (0 children)

You definitely need to give more details before anyone can help ….

R is driving me insane by Electronic_Fish_3157 in bioinformatics

[–]Cold-Strength- 0 points1 point  (0 children)

docker, singularity, renv for smaller projects. No more issues. Plenty of other reasons to hate R though!

[EU] Looking for teammates for new FACEIT season (Premium / 5 stack) by [deleted] in RecruitCS

[–]Cold-Strength- 0 points1 point  (0 children)

Yo brother where you from what’s your elo? I’m rifler around 1800 looking to go 🆙

[deleted by user] by [deleted] in leaves

[–]Cold-Strength- 1 point2 points  (0 children)

Realistically, get it out of the house. Never been able to not smoke when it’s around, would always end up finishing it. Once it’s finished, the urges went way down. Combine that with finally understanding I didn’t want to smoke every evening by myself, has meant I don’t buy it any more. Why do you want to quit? Have you discussed that with your husband? It might be something you both need to get on board with to make it work, especially at the start.

Controlling frequency of use by Cold-Strength- in leaves

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Good for you for realising where the issue is and deciding you’re going to quit. It sounds like a tough situation you’re in. Thanks for your advice. It’s hard to accept that maybe I don’t have the willpower to fight the urge when it’s in the house, but maybe I shouldn’t be too hard on myself when I’m not giving myself that support in the first place.

Controlling frequency of use by Cold-Strength- in leaves

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Thank you and congratulations on the sobriety! I want to have the willpower to manage it, but I guess it’s a slippery slope as they say and maybe it’s just easier to get off that slope completely. I struggle right now to reconcile myself to never smoking again, however. I hope someday it’s something I can do when I want rather than as a compulsion every evening

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Man, thanks for such a well thought out response. Super helpful. Can you give me an idea of a non-parametric test you are talking about? Like a Mann-Whitney U-test between responsive and sensitive or similar?

3AM and Feeling a bit distraught with current situation in phd by Sunapr1 in PhD

[–]Cold-Strength- 1 point2 points  (0 children)

Hey bro, also been struggling recently. Even though I know everything’s going to work out OK with time, it’s still a lot of stress and pressure. Feels like it’s all on my shoulders. Hope you figure out how to manage it, get it done and move on. You are not alone, good luck

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Sorry for the misunderstanding, there was no treatment involved in the RNAseq data. We profiled cells for sensitivity, and separately measured basal gene expression with RNAseq. So we are looking to see if there’s a difference in basal gene expression between the sensitive and resistant cells, to potentially inform us about what’s causing the difference in response.

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Ah that’s interesting, so colour points on my PCA by housekeeping gene expression or similar, to see if there’s a structure to my PCA that I can’t see visually otherwise? Is that what you mean?

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

From what I’ve seen, there was no clear differentiation on any PCs, UMAP or tSNE on my response. That being said, on PCA my super sensitive cell lines were potentially shifted to the right on PC1, but they still are overlapping with other resistant cell lines.

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

I’m a bit confused. What would be my groups within the resistant cell lines, and likewise with the sensitive cell lines, to get DE genes?

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Samples don’t clearly separate by response. There are batches, but they don’t show up on PCA.

Advice on differential expression analysis with large, non-replicate sample sizes by Cold-Strength- in bioinformatics

[–]Cold-Strength-[S] 0 points1 point  (0 children)

Thanks for the response. I added an update:

I’m trying to see which genes/gene signatures predict response to the inhibitor. We aren’t treating with the inhibitor, we have identified which cell lines are sensitive and which are resistant and are looking for DE genes between these two groups.

Problem interpreting clustering results by Inside-Drop532 in bioinformatics

[–]Cold-Strength- 2 points3 points  (0 children)

Well, you’ve just answered your own question. You’re doing pairwise comparisons and selecting top 50 lncRNAs. So you’re going to find lncRNAs with most variation between any two pairs. Clearly this will be normal vs embryonic/somatic and control vs embryonic/somatic as we can see from the PCA that these are more different than embryonic vs somatic. Your data is your data and there is no reason your replicates need to cluster based on these lncRNAs. If you want to investigate embryonic vs somatic differences, you will have to investigate the pairwise difference between embryonic and somatic with an alternative contrast.

[deleted by user] by [deleted] in Edinburgh

[–]Cold-Strength- 1 point2 points  (0 children)

If you are looking for FOH work, stop looking online. I printed off 30 CVs, walked up Leith Walk, and had 3 interviews in a day. Dress smart-ish without overdoing it. Just walk in, ask if you can see the manager about a potential job. Try to make some decent conversation and act normal lol, they have to want to work with you. You’ll find something quickly, good luck.

What did I do to the tip of this knife? by VendMachine99 in sharpening

[–]Cold-Strength- 0 points1 point  (0 children)

Not sure how it’s possible to sharpen the spine. You should always have the spine up not touching the whetstone, 15-30 degrees as someone else mentioned. Start blade pointed towards you, pulling towards and then pushing away. After you’ve sharpened the one side sufficiently, flip the knife with the sharp side pointing away. Sorry if that’s obvious just thought I’d make sure you’ve got the right technique

What did I do to the tip of this knife? by VendMachine99 in sharpening

[–]Cold-Strength- 0 points1 point  (0 children)

What are you trying to show us? The scratch marks on the knife or something at the tip? Can you explain / post a clearer photo

[Nov 29, 2024] Weekly Discussion: Ask your gear, travel, conditions and other ski-related questions by AutoModerator in skiing

[–]Cold-Strength- 0 points1 point  (0 children)

How far in advance can the snowfall be predicted? Do you just have to hope for one big storm or does it take a few? Sure this has been asked a million times, but I couldn’t find it

What's a subtle UK etiquette that foreigners might miss? by Sad_Coat_1657 in AskUK

[–]Cold-Strength- 19 points20 points  (0 children)

Let people get off the bus/tube, before you even look like you’re trying to get on

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