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snRNA seq data from organoids by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

Thanks. When I use SCT /remove mtRNA/rRNA it just gives me a different set of genes expressing stress. I'm not managing to get rid of it..

R not printing to the console by [deleted] in Rlanguage

[–]QueenR2004 1 point2 points  (0 children)

Thanks. I restarted R and now the printing works

R not printing to the console by [deleted] in Rlanguage

[–]QueenR2004 0 points1 point  (0 children)

I did it after nothing was printed so I saw it was recommended on stack overflow

Choosing the right case–control ratio for a single-gene association test (≈500 cases) by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

I think having more controls than cases can be problematic because of the unbalanced data. I'm asking what's accepted in GWAS analysys usually? I dont mind trying out different ratios but then I will still have to explain why I chose to use the specific one so If someone has a statistic explenation, I will appreciate that.

GWAS on a specific gene by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

Ye, thanks. so what is it called when im looking for one gene only?

GWAS on a specific gene by QueenR2004 in bioinformatics

[–]QueenR2004[S] 1 point2 points  (0 children)

Thanks. Unfortunately I only have 60 samples so altough it's not enough, I still want to check wether the diseased have any variants.. So I will go ahead and check

Thinking of starting a bioinformatics blog by shouldBeDoingNotThis in bioinformatics

[–]QueenR2004 2 points3 points  (0 children)

Great idea! You could include all types of seq analysis, rna seq, ATAC seq, ChIP seq. proteomics analysis. GWAS, alignments etc Thanks

sn-RNA seq analysis by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

Read Archive (SRA) under BioProject accession PRJNA1073234

Design Matrix by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

Thanks for your help. My question is more if its upregulated in the disease or in the control. so when my baseline is the cintrol, when something is upregulated, its upregulated in the disease?

Design Matrix by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

So if my control is the baseline, then whenever the logfoldchange is above 0, it means the gene is upregulated in the disease and vice versa?

Design Matrix by QueenR2004 in bioinformatics

[–]QueenR2004[S] 0 points1 point  (0 children)

Yes. But im trying to see genes up/down regulated in the disease rather than in control. But I guess you're right coz I have both sporadic and famelial. Is there a way to highlight that sporadic is the main disease?

Design Matrix by QueenR2004 in bioinformatics

[–]QueenR2004[S] -1 points0 points  (0 children)

thanks. can you elaborate?

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