User: fruce_ki

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fruce_ki20
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Austria/Vienna/Research Institute for Molecular Pathology
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fruce_ki
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Kimon Froussios, PhD

Bioinformatician

Posts by fruce_ki

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... DGE and DTU are different things, regulated by different mechanisms. You can have one or the other or both. I would not normally expect a high overlap between DGE and DTU genes. ...
written 3 months ago by fruce_ki20
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... Also, I'm not sure why you are using the g.test.2 function directly. Do you only have one gene to test? You should use TPMs scaled to the size of the sample's library, but I'm not sure what "problem" you think this will fix. You didn't mention a problem, it was just a question about test design. ...
written 3 months ago by fruce_ki20
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... You can have any combination of DGE and DTE and DTU going on at the same time, and they are all valid. In your example, you have one DTE isoform (from 100 to 5000) and the whole gene being DGE (from 600 to 5500) andv the gene also being DTU (from 0.17/0.33/0.5 to 0.91/0.04/0.05). That isoform will ...
written 3 months ago by fruce_ki20
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Answer: A: Difference between gene-level test and transcript-level test with RATs (Relative
... Hi, Thank you for taking an interest in RATs. Say you have two conditions A and B and a gene with isoforms 1, 2, 3, etc... The gene level test compares the full set of abundances (A1, A2, A3, ...) against the full set of abundances (B1, B2, B3, ...). This can tell you in which genes the ratios ch ...
written 3 months ago by fruce_ki20
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Comment: C: Not getting the expected answers from GenomicRanges follow/precede
... I did look at the docs repeatedly, though not carefully enough it seems. I focused on the strand orientation bit, which can also have the effect of giving the seemingly opposite answer. Friday evening overtime probably not the best time to be learning new things. So the query precedes or follows th ...
written 2.1 years ago by fruce_ki20 • updated 2.1 years ago by Martin Morgan ♦♦ 23k
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Not getting the expected answers from GenomicRanges follow/precede
...   I'm getting the opposite answer than I would expect. This has nothing to do with getting opposite behaviour between '+' and '-' strand. My problem here is all on the  '+' strand.   # Subject ref <- GenomicRanges::makeGRangesFromDataFrame( structure(list(seqnames = structure(c(1L, 1L, 1L ...
genomicranges written 2.1 years ago by fruce_ki20 • updated 2.1 years ago by Valerie Obenchain6.7k
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Comment: C: How to preserve the strand of coverage in derfinder::regionMatrix() ?
... I feared as much. That is the conclusion we reached in my lab too. So that's what I'm looking into, indeed. I was hoping there might have been an easier way. Oh well...Thanks! At least now I know I'm not overcomplicating it. ...
written 2.1 years ago by fruce_ki20
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How to preserve the strand of coverage in derfinder::regionMatrix() ?
... I am using derfinder (in region mode) for annotation-free DE. Then I want to match the DE regions to the nearest *upstream* known gene. For this it is important to know which strand the coverage is on. However regionMatrix() produces regions that have no strand information. The result of fullCovera ...
derfinder written 2.1 years ago by fruce_ki20 • updated 2.1 years ago by Leonardo Collado Torres690
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... Ok, that clears it up quite a bit. Many thanks! ...
written 2.1 years ago by fruce_ki20
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Comment: C: IRanges error from derfinder analyzeChr with custom TxDb?
... So what is the recommended/most efficient usage case? Should I use only one of the two options? Like set the desired cutoff right from the load and unset the cutoffPre?  Or maybe set both to the same value? Or is cutoffPre ignored when the data is already filtered and no subsetting is requested? ...
written 2.2 years ago by fruce_ki20

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