User: Lila M
Lila M • 900
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Posts by Lila M
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... Hi there,
I was wondering which could be the best approach to correlate expression levels (from RNA -seq) mutated genes and clinical variables for a specific patients data set.
I have two data frames, let's call them `exp` with the typical RNA-seq data processed by `DESeq2` and other table with g ...
written 21 hours ago by
Lila M • 900
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... because there is no other kind of analysis than can be done with the RNA seq apart from DE to test this kind of differences, right? ...
written 5 days ago by
Lila M • 900
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... It is an in-house method who is very reliable actually (can't explain so far). It has not be tested as DE in lab, but the genes have an effect ...
written 5 days ago by
Lila M • 900
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... Hi all,
I have the RNAseq data for an experiment, with data under two condition. I've performed the typical DE analysis using `DESeq` in `R`. On the other hand, I have a positive control genes from the lab, but unfortunately, those genes are not DE in my analysis. So now, I'm wondering if there is ...
written 5 days ago by
Lila M • 900
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Comment:
C: LEfSe for multiple samples
... you can try [this][1]. Other option is to use [Galaxy][2] m that has a very good implemented interface to address this issue. Is less manipulative but is very straight forward
[1]: https://rdrr.io/github/ying14/yingtools2/man/lefse.html
[2]: https://huttenhower.sph.harvard.edu/galaxy/ ...
written 5 days ago by
Lila M • 900
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Comment:
C: LEfSe for multiple samples
... You can use `lefser` for that propose. Have a look into the argument `one.against.one : for multiclass tasks, sets whether testing is performed one-against-one (TRUE - more strict) or one-against-all (FALSE - less strict)`
So if you have 5 groups: A,B,C,D and E, for the `all-against-all` featu ...
written 6 days ago by
Lila M • 900
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... yes but I get the same result :( ...
written 4 weeks ago by
Lila M • 900
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... my bad, the original table is `xx` and `mat` is the matrix that I can't get ...
written 4 weeks ago by
Lila M • 900
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... No, there is not a duplication for every gene ...
written 4 weeks ago by
Lila M • 900
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... It creates an empty table ...
written 4 weeks ago by
Lila M • 900
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