User: e.rempel
e.rempel • 890
- Reputation:
- 890
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- Germany, Heidelberg, COS
- Last seen:
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- Joined:
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Statistician/bioinformatician.
Posts by e.rempel
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... Upvote for the first sentence. ...
written 14 days ago by
e.rempel • 890
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... Hi,
p-value cutoff is specified in the entry dba.object$config$th. You can directly change it
dba.object$config$th <- .01 ...
written 14 days ago by
e.rempel • 890
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... > arguments imply differing number of rows: 0, 6
meaning that the object *sampleFiles* is likely to be empty (it has 0 rows). What is the output of `list.files(directory)`? ...
written 15 days ago by
e.rempel • 890
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... I assume, there is something wrong with *sampleTable*, e.g. the column *condition* has only 2 entries, but shouldn't it have 6? What is the output of just *sampleTable*?
Edit: it looks like you forgot to remove the line
directory <- system.file("extdata", package = "pasilla", mustWork = TRU ...
written 15 days ago by
e.rempel • 890
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... Have a look [here][1]
[1]: https://stackoverflow.com/a/18509816/4763043 ...
written 20 days ago by
e.rempel • 890
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... I think, the column *weightFisher* contains the p-value. ...
written 20 days ago by
e.rempel • 890
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... Hi,
it is possible to specify your design with one condition column, but it is more meaningful to use two conditions 'gene A' and 'gene B' (or factors in the lingo of DESeq) with two factor levels each ('transfected' or 'not transfected'). Then it is possible to use the design formula in my origina ...
written 20 days ago by
e.rempel • 890
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... Hi,
rather a comment than a full answer.
I think, you could use an interaction term in your design formula. Something like
design(dds) <- ~ geneA + geneB + geneA:geneB
Also, have a look [here][1]
[1]: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#in ...
written 22 days ago by
e.rempel • 890
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Comment:
C: Statistical test for overlap
... In this case shouldn't it be `p = (5224 + 309)/(5224 + 309 + 5646 + 108)` ? :) ...
written 24 days ago by
e.rempel • 890
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... Or [Fisher's exact test][1]
[1]: https://en.wikipedia.org/wiki/Fisher%27s_exact_test ...
written 24 days ago by
e.rempel • 890
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