User: e.rempel

gravatar for e.rempel
e.rempel900
Reputation:
900
Status:
Trusted
Location:
Germany, Heidelberg, COS
Last seen:
2 weeks, 2 days ago
Joined:
5 years, 6 months ago
Email:
e*******@dkfz-heidelberg.de

Statistician/bioinformatician.

Posts by e.rempel

<prev • 104 results • page 1 of 11 • next >
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Comment: C: aligning with STAR
... Yes, you are right, I change it. ...
written 5 weeks ago by e.rempel900
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Comment: C: Dragen alignment failing/terminating
... Strange, for me it looks like the alignment ran through successfully, e.g. MAPPING/ALIGNING SUMMARY Number of unique & mapped reads (excl. dups) 2228837529 97.24 ...
written 9 weeks ago by e.rempel900
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Comment: C: Help with my differential expression analysis (homework)
... Upvote for the first sentence. ...
written 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900
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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 4 months ago by e.rempel900

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Scholar 4 months ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to create a design matrix for Cpg.annotate?
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: GO analysis using topGO Arabidopsis
Scholar 5 months ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
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Pundit 13 months ago, created a comment with more than 10 votes. For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
Popular Question 13 months ago, created a question with more than 1,000 views. For bcl2fastq creates only Undetermined fastq
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