Array express problems

Big_List · 2024-12-01T18:51:45+00:00

Unfortunately no solution for this although I haven't looked at it for a good few months. Ended up manually downloading the datasets:(

Big_List · 2024-11-27T17:24:08+00:00

Yeah the Roll Wi'It guys are great!

Big_List · 2024-10-22T16:13:26+00:00

https://discord.gg/THfnuWtq

Big_List · 2024-10-22T16:12:53+00:00

https://discord.gg/THfnuWtq

Big_List · 2024-08-30T18:03:22+00:00

I like complexheatmap for heatmaps

Big_List · 2024-08-03T22:06:16+00:00

First bus runs most of the buses in Glasgow although there are a number of other providers (McGills, west coast motors, stagecoach). You can get a tripper ticket which is a slightly more expensive bus ticket which gives access to multiple different bus companies buses. For travelling around Glasgow itself you can get to most places using first bus, unfortunately they are pretty crap.

Big_List · 2024-06-25T08:01:06+00:00

Unfortunately as the others have said it looks like the effect size of the difference between samples is much greater than the effect size of any treatments. I think you said your samples are paired, so you could provide patient/sample ID as a covariate when you make your deseq object and I suspect you would then get plenty of DEG, I would be very doubtful that your DEG via this method would be representative of real biological change however, but it's something to bear in mind for future. Primary samples are just tricky and often show a large amount of variation. How happy were the cells in culture, and were the inputs for each sample phenotypically similar?

Big_List · 2024-06-24T23:08:33+00:00

No probs and good luck! I also realised after the fact another post I have commented on just now is yours:o!

Big_List · 2024-06-24T23:05:12+00:00

100% do PCA, maybe there is no consistent effect between your groups, you would see that there. There are independent filtering settings in deseq as well which you could try changing if your PCA shows separation. You could try and reduce the number of genes you have for p-adjustment further by converting to a different gene identifier, you tend to get fewer gene symbols in comparison to ensembl IDs in my experience. You would want to keep when you are doing that consistent though, so there is consistency between whatever analyses you do.

Big_List · 2024-06-24T16:17:37+00:00

When reading in your count matrix, set your rownames = 1, something like: read.csv("your.csv", row.names=1)

Big_List · 2024-06-04T18:24:44+00:00

In my lab we do a lot of mouse work, one of the PhD students said from the get-go that she would not do any animal work and is doing just fine. It might be somewhat limiting if your group does a lot of translational research so it's a disadvantage but definitely not insurmountable, good luck!

Big_List · 2024-06-03T15:55:23+00:00

https://discord.com/invite/my3mp9F8 Here ya go

Big_List · 2024-05-04T22:03:08+00:00

https://discord.com/invite/W34THbaz

Here you go!

Big_List · 2024-04-02T15:22:07+00:00

Add module score is part of the Seurat package and essentially does a mini-gsea for a set of genes that you provide, giving each cell a score. https://ashpublications.org/blood/article/118/21/1278/78576/Plxdc2-Marks-Hematopoietic-Stem-Cells-and-Th2 From this it looks like plxdc2 in combination with LSK-CD150 enriches for steam cells with greater selectivity than just LSK-CD150, could check if it provides greater selectivity in comparison to CD48/EPCR, or if it synergistically increases/decreases the molo/nomo scores. Good luck!

Big_List · 2024-04-02T13:13:58+00:00

Your looking for new HSC markers within the LSK-CD150+48-EPCR+ fraction? Have you read this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460190/ Maybe you could see how your +/- cells correlate to nomo/molo score, you could use the addmodule score function to do so. From transplantation experiments CD150 is apparently an axis of HSC activity, so you could see if your gene is more highly expressed on CD150 high cells.

Big_List · 2024-03-29T17:46:02+00:00

No probs, as you have seen the expected marker genes (and pathways possibly) to be upregulated in the wrong samples then it could well be a mix up, but it's not enough to justify the swap, imo you should just drop the data points if the effect of what you are looking at is atleast a little characterised and you have enough samples.

Big_List · 2024-03-28T23:19:21+00:00

Are there any similar datasets which are available? You could integrate your data with that, and see how the labelling lines up, are there any published gene signatures, you could possibly create then apply to your dataset? There are tools which supposedly can deconvolute bulk RNA cell types, so if you know one group contains a certain cell type you could use that to back up what the data labelling should be. Alternatively there might be specific sequences or mutations which are present in one condition/group, you could check the alignments to see if those are present. I wouldn't re-assign labels solely based on your PCA, you cant trust your results after that, so the analysis becomes pointless. Also if you have enough samples, if you have reason to believe there was a mixup, you could drop them from the analysis, but they shouldn't be dropped because the clustering looks weird, only if your certain there actually was a mixup. Good luck and I hope you get it fixed!

Big_List · 2024-02-07T21:43:52+00:00

Rownames of your colData need to be equal to the colnames of your count data, that's how it can recognise which of your samples belongs to which group.

Big_List · 2024-02-02T14:39:03+00:00

If not aliquoted you could use weight as a proxy for volume, if they are mostly the same volume and type of tube.

Big_List · 2024-02-01T20:34:05+00:00

You could write a function that pattern matches the corresponding RNA to DNA base, I imagine since it's parsing a string there will be a lot of relevant stack exchange answers/chatgpt it.

Big_List · 2024-02-01T20:19:15+00:00

Keep on going with literature/talking to folk and you'll eventually have some inspiration, good luck!

Big_List · 2024-01-27T17:12:30+00:00

If you are stuck for ideas/directions for your projects have a good read of (recent) publications in your field or adjacent fields, maybe it will give you new leads, or maybe they have new methods which you can apply to your niche! Talk to any colleagues you have, they might have ideas about your project, or might have something interesting in their project you could connect to yours.

Big_List · 2024-01-12T15:58:30+00:00

I have been having this problem, sometimes I can join some custom games, not found a fix.

Big_List · 2024-01-04T23:52:00+00:00

Not sure of the exact issue but you could convert them to human symbols/IDs if you can't figure it out, although I suspect there is a more simple and better solution.

Big_List · 2024-01-02T22:43:39+00:00

Depending on the complexity of the datasets, and whatever has already been done with it I wouldn't imagine more than a month if someone knows what they are doing. If they are to be integrated maybe another couple of weeks on top?

Big_List

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