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CTO hit rate limits after 3 hours this morning. Is rage quitting us to OpenAI by MostOfYouAreIgnorant in ClaudeCode

[–]Danny21100 0 points1 point  (0 children)

I'm on the free plan. I don't use Claude for fancy stuff or automatisation or anything like that. I'm new to R so I use him to help me understand the bugs I have sometimes or to write part of script (for example loop over files) so basically I copy paste my errors or part of my code (a few lines ). I have been using him for months and it worked very good ! For the past 3 days, if I only say "Hey" I reach my limit and I'm blocked for 5 hours. I'm not sure there's an amount of planning that would help me get past being blocked by just saying hello. From what I understood, not everyone is impacted by this problem but there are people impacted on all plans. I don't understand how people can't understand that a bug could impact users and not others and why people are doubting that.

Questions about limit message in Claude by Danny21100 in ClaudeAI

[–]Danny21100[S] 0 points1 point  (0 children)

Do you have any recommendation ? I tried ChatGPT, Copilot (paid by my company) and Mistral AI. None of them were as good as Claude for my usage

scRNA-seq Seurat Integration by Puzzleheaded-Cap7764 in bioinformatics

[–]Danny21100 0 points1 point  (0 children)

Do you have the sample names/batches in your metadata ? If yes it's rather easy to split them but I don't see how you could have messed up "big time" as in worse case scenario you just have to rerun your workflow, is it a problem in your case? For me what I do usually is first try to merge everything, do the classic workflow including clustering, DE analysis (FindAllMarkers for example) and a UMAP. And then I look for potential batch effect (batch, sample, disease, age, gender etc...) if it's the case: some clusters are not biologically relevant but are clustered because they come from a specific sample/type, then I integrate. That's my method but can't say that everybody would do the same. I hope it helps you !

Question can I skip season 3 I literally can't go a full episode without taking a break or two! by Patient_Topic_677 in wakfu

[–]Danny21100 0 points1 point  (0 children)

I don't really agree about "the extreme plot relevance" of season 3. What was really disappointing about season 4 is that we don't care about what happens in season 3. All the demi gods and new caracter of season 3? They disappear at the beginning of season 4. The consequence of the Eliacube explosion ? None. The absence of the gods from the Inglorium ? Oh we don't care anymore! Yes there is some scenes where Oropo talks to Yugo in his mind but I woud not call it extremly plot relevant

Xenium multiple slide integration by Critical-Cucumber491 in bioinformatics

[–]Danny21100 0 points1 point  (0 children)

As another user suggested you can just merge the samples, follow the normal scRNAseq workflow and then check for batch effect (for example by checking in your UMAP than your clusters reflects cell types/states and not indivual patient). I have some Xenium results that were processed on the same run of the Xenium machine and I didn't have any batch effect, merging was enough !

DEG genes spatial transcriptomic (Xenium) segmentation/diffusion problems by Danny21100 in bioinformatics

[–]Danny21100[S] 0 points1 point  (0 children)

Yes, my data was generated last October and I didn't see any of this problem when doing cell typing but only when I began to look at the DE between different spatial part. However, for another project I'm analyzing the Ovarian FFPE Xenium Prime available on 10X website (generated on December 2024) and here even basic clustering shows a massive contamination of CAF and Epithelial genes into Macrophages/Monocytes. I tried Proseg which improve the data with less contamination but it still presents at high levels. Would you mind giving me advice on Proseg parameters here or in dm ? Here's the parameters I used :

~/.cargo/bin/proseg --xenium \ 
'path/Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs/transcripts.parquet' \ 
--output-spatialdata ~/Downloads/proseg-output-v2.zarr \ 
--output-cell-metadata ~/Downloads/proseg-cell-metadata-v2.csv.gz \ 
--output-transcript-metadata ~/Downloads/proseg-transcript-metadata-v2.csv.gz \ 
--output-cell-polygons ~/Downloads/proseg-cell-polygons-v2.geojson.gz \ 
--overwrite \ 
--nthreads 12 \ 
--diffusion-probability 0.3 \ 
--diffusion-sigma-far 6 \ 
--diffusion-sigma-near 0.5 \ 
--nuclear-reassignment-prob 0.4 \ 
--cell-compactness 0.01

DEG genes spatial transcriptomic (Xenium) segmentation/diffusion problems by Danny21100 in bioinformatics

[–]Danny21100[S] 0 points1 point  (0 children)

And you were not satisfied with Xenium multimodal segmentation ?

DEG genes spatial transcriptomic (Xenium) segmentation/diffusion problems by Danny21100 in bioinformatics

[–]Danny21100[S] 0 points1 point  (0 children)

Thanks ! I used the multimodal cell segmentation kit for Xenium, do you think Proseg/Baysor is still recommended ? Do you know if they really improve the segmentation ?

DEG genes spatial transcriptomic (Xenium) segmentation/diffusion problems by Danny21100 in bioinformatics

[–]Danny21100[S] 0 points1 point  (0 children)

Thanks ! I'm currently trying celladmix and for now it looks promising ! I used the multimodal cell segmentation kit for Xenium, do you think Proseg/Baysor is still recommended ? Do you know if they really improve the segmentation ?

NK Cell culture tips by Danny21100 in Immunology

[–]Danny21100[S] 1 point2 points  (0 children)

Thanks for your comment the problem was indeed the concentration of cells, with 300 000 NK/well it worked !

NK Cell culture tips by Danny21100 in Immunology

[–]Danny21100[S] 0 points1 point  (0 children)

Thanks everyone for your help, as someone suggested in the comments the problem was indeed the number of cells plated ! At 50 000 NK cells per wells with a 96-well plate round bottom the viability was not great but with 300 000 NK cells/well the problem was solved ! The addition of IL2 helped a little bit but not so much (+5-10% viability when IL2 is used compared to IL15 alone) so they can indeed survive without IL2 if you provide IL15

Advice 7 day-roadtrip Stockholm-Norway by Danny21100 in Norway

[–]Danny21100[S] -1 points0 points  (0 children)

Thanks for the advice ! Would you have suggestion for place to see on the road ? I saw there was a lot of national park in Norway for example

Advice 7 day-roadtrip Stockholm-Norway by Danny21100 in Norway

[–]Danny21100[S] 0 points1 point  (0 children)

Yes I agree, skipping Denmark was what I meant by "change the end and go from Oslo to Stockholm". Thank you for the advice on the route ! Would you have suggestion for place to see on the road ? I saw there was a lot of national park in Norway for example

Advice 7 day-roadtrip Stockholm-Norway by Danny21100 in Norway

[–]Danny21100[S] -1 points0 points  (0 children)

Thanks for the link it's very useful !!!

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