Moderator: ATpoint
ATpoint ♦ 46k
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... Check http://bioconductor.org/books/release/OSCA/normalization.html#normalization-by-deconvolution
It is an awesome read for basically everything related to scRNA-seq with regard to the Bioconductor universe. ...
written 2 days ago by
ATpoint ♦ 46k
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... The vst is for UMI data though, you would need to check whether all platforms have that. I would use the method in `scran` though tbh as it corrects for compositional changes which you almost certainly will have as different single-cell platforms have different ways of capturing and processing the t ...
written 2 days ago by
ATpoint ♦ 46k
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... I think you will have a hard time trying to tweak the data for your purposes. Single-cell assays can suffer from severe batch effects between experiments. It is possible to integrate assays, with tools such fastMNN, but this usually results in corrected values in PCA space which can then be used to ...
written 2 days ago by
ATpoint ♦ 46k
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... Warning: tl:dr will follow but I guess some background information might be appreciated.
=> Salmon quantifies against a transcriptome, so the `quant.sf` are transcript abundance estimates. One commonly performs analysis with DESeq2 on the gene level though. The reason is that:
a) it is more str ...
written 2 days ago by
ATpoint ♦ 46k
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... Please use `ADD REPLY`, the answer box is for answers only. That keeps it logically organized. ...
written 2 days ago by
ATpoint ♦ 46k
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written 3 days ago by
ATpoint ♦ 46k
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... > I thought about doing ~ sample_time + treatment but I am thinking that I might have problem with all treated samples collected later than the control ones and being unable to separate that from the effects of the treatment. What would be the best way to approach this?
Yes, you cannot control f ...
written 3 days ago by
ATpoint ♦ 46k
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... Do the different datasets contain roughly the same celltypes or is this rather a mishmash of experiments? ...
written 3 days ago by
ATpoint ♦ 46k
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... This is RNA-seq, not microarrays which GEOquery assumes, so it is expected that it produces no output.
RNA-seq is sequencing data, you therefore will need to download the fastq files, align/quantify to get a matrix of raw counts.
For starters maybe this paper: https://peerj.com/preprints/27283/
Pl ...
written 3 days ago by
ATpoint ♦ 46k
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... https://stackoverflow.com/questions/13575180/how-to-change-language-settings-in-r ...
written 3 days ago by
ATpoint ♦ 46k
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