User: e.rempel
e.rempel • 900
- 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
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Comment:
C: aligning with STAR
... Yes, you are right, I change it. ...
written 5 weeks ago by
e.rempel • 900
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... 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.rempel • 900
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... Upvote for the first sentence. ...
written 4 months ago by
e.rempel • 900
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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 4 months ago by
e.rempel • 900
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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 4 months ago by
e.rempel • 900
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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 4 months ago by
e.rempel • 900
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... Have a look [here][1]
[1]: https://stackoverflow.com/a/18509816/4763043 ...
written 4 months ago by
e.rempel • 900
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... I think, the column *weightFisher* contains the p-value. ...
written 4 months ago by
e.rempel • 900
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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 4 months ago by
e.rempel • 900
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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 4 months ago by
e.rempel • 900
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For A: How to create a design matrix for Cpg.annotate?
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For A: How to create a design matrix for Cpg.annotate?
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For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
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For bcl2fastq creates only Undetermined fastq
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