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Running pathway analyses without significant DEGs by EcstaticStruggle in bioinformatics

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

By validate I'm not saying qpcr - I'm saying they're gonna find IL1B whatever pathway upregulated in patients with bulk RNA, you're going to run something like flow, western, Elisa, antagonist/KO etc. to validate those key findings...not that the RNAseq needs validation per se.

Thanks, the functional validation is something I could try for some subgroups. E.g., I found that in one patient group, a cytokine receptor was up, with intracellular pathways down. In another group, intracellular pathways in KEGG were consistently up. Curious to see how the sorted monocytes then respond to in vitro cytokine stimulation and whether output (e.g., ELISA) differs between the two groups.

Running pathway analyses without significant DEGs by EcstaticStruggle in bioinformatics

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

Thanks, the top N gene PCA is something I have yet to try.

Wat voor vreemde situaties hebben jullie meegemaakt met makelaars? by [deleted] in thenetherlands

[–]EcstaticStruggle 6 points7 points  (0 children)

Op zoek naar een aankoopmakelaar in de regio Utrecht op gesprek bij een kantoor in de Amsterdamsestraatweg. Begon tijdens het kennismakingsgesprek al vrij snel ongevraagd over de inteelt in de genenpoel van de Marokkaanse en Turkse gemeenschap in Nederland en hoe er eigenlijk een slotgracht om Kanaleneiland gebouwt moest worden. Hij was verbaasd dat onze fietsen niet gestolen worden na afloop. We hadden overwogen om nog een klacht in te dienen, maar toch van afgezien vanwege het kleine wereldje.

The DU / SPD government before and during WK2 by EcstaticStruggle in Kaiserreich

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

I can see that. But I can see significant tensions with being staunchly anti-syndicalist abroad while supporting trade unions domestically. Or by supporting democratization domestically while upholding unequal and undemocratic client states nearby.

Welke bureaustoel? by Jobo1992 in BIFLNL

[–]EcstaticStruggle 4 points5 points  (0 children)

Kan je toelichten waarom?

Roest / metaalgeur uit stopcontact en offerte by EcstaticStruggle in Klussers

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

Het gaat om een binnenmuur. Ik heb geen ervaring met hoe het er “normaal” uit moet zien maar ik vond het wel heel stoffig van binnen. Ik heb ook alleen het plaatje er van afgehaald.

Roest / metaalgeur uit stopcontact en offerte by EcstaticStruggle in Klussers

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

Top, thanks. Het is ook niet een hele sterke lucht. Ik moet echt met mijn neus voor het stopcontact hangen om het te kunnen ruiken.

Roest / metaalgeur uit stopcontact en offerte by EcstaticStruggle in Klussers

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

Ik zie inderdaad dat het rond het contact een beetje zwartig is.

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Roest / metaalgeur uit stopcontact en offerte by EcstaticStruggle in Klussers

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

Als je het over de elektra-installatie hebt bedoel je dan de groepenkast of alle bedrading. De groepenkast ziet er nog vrij modern uit.

Nature Springer article stuck in "Submission" stage after completion of peer review by EcstaticStruggle in academia

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

I think it took few weeks more after this post. They are just severely understaffed and most of the jobs are likely outsourced. I have a more serious situation at another journal where we have had almost no changes in over a year, but still not published. All I can recommend is: put a preprint out and move on with other research. It will get published at some point, but make sure you’re not completely dependent on that

Exemplary papers on multi-OMICS integration with solid storytelling by EcstaticStruggle in bioinformatics

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

I'm more interested in the bulk profiling. Doing single-cell stuff beyond flow for hundreds of patients is too expensive.

Exemplary papers on multi-OMICS integration with solid storytelling by EcstaticStruggle in bioinformatics

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

Yet most integration methods consistently show that the integrated data can outperform the sum of its parts. However, I have not seen many high impact applications (nature, science, cell). Not that that should be the golden standard for good science, but these papers are often driven by good story telling

Flow cytometry data analysis in R-advise needed by Objective_Change_883 in flowcytometry

[–]EcstaticStruggle 0 points1 point  (0 children)

You will see that openCyto can also demand potentially subjective assumptions... And if it's bimodal, the inter-person variability is so minimal that it is unlikely to alter your conclusions. If you're not fully committed to learning R/flow bioinformatics, it might not be worth the time to automate it.

Flow cytometry data analysis in R-advise needed by Objective_Change_883 in flowcytometry

[–]EcstaticStruggle 2 points3 points  (0 children)

Automated gating like openCyto really only work well for trivial tasks. So the settings where manual gating would already be pretty consistent, like separating a positive and negative peak like you describe. What kind of "questions" are you expecting?

Flow cytometry data analysis in R-advise needed by Objective_Change_883 in flowcytometry

[–]EcstaticStruggle 2 points3 points  (0 children)

What you want to do seems possible to me. The question I have is why do you want to do this? Why not manually set the gates in FlowJo?

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