User: e.rempel

gravatar for e.rempel
e.rempel890
Reputation:
890
Status:
Trusted
Location:
Germany, Heidelberg, COS
Last seen:
1 day, 4 hours ago
Joined:
5 years, 3 months ago
Email:
e*******@dkfz-heidelberg.de

Statistician/bioinformatician.

Posts by e.rempel

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Help with my differential expression analysis (homework)
... Upvote for the first sentence. ...
written 14 days ago by e.rempel890
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Answer: A: How to change the default P value and FDR cutoff in DiffBind
... 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.rempel890
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Comment: C: DESeq DataSet from HTSeqCount Error
... > 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.rempel890
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Comment: C: DESeq DataSet from HTSeqCount Error
... 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.rempel890
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Comment: C: <DESeqDataSet>[i,] index out of bounds - subsetting DESeqDataSet
... Have a look [here][1] [1]: https://stackoverflow.com/a/18509816/4763043 ...
written 20 days ago by e.rempel890
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Comment: C: How do I extract the p-value from runTest() in the TopGO package?
... I think, the column *weightFisher* contains the p-value. ...
written 20 days ago by e.rempel890
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Comment: C: Design for a two-gene mechanism in DESeq2
... 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.rempel890
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Answer: C: Design for a two-gene mechanism in DESeq2
... 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.rempel890
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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.rempel890
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Comment: C: How to check if there is an association between clustering output (groups) and p
... Or [Fisher's exact test][1] [1]: https://en.wikipedia.org/wiki/Fisher%27s_exact_test ...
written 24 days ago by e.rempel890

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Scholar 20 days ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How to create a design matrix for Cpg.annotate?
Scholar 24 days ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: GO analysis using topGO Arabidopsis
Scholar 6 weeks ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
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