User: ddiez

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ddiez1.7k
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Posts by ddiez

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Comment: C: Remove Surrogate Variables and Batch
... Take a look at `?limma::removeBatchEffect` for details of other uses of the processed dataset. For differential expression it is better to use the original dataset and add batch as covariate, as indicated in @jtleek's answer. ...
written 10 months ago by ddiez1.7k
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Comment: C: Need help plotting D statistics
... Also consider using `geom_text_repel()` in the [ggrepel package][1]. See for example the vignette [here][2]. [1]: https://cran.r-project.org/package=ggrepel [2]: https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html ...
written 14 months ago by ddiez1.7k
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Comment: C: Need help plotting D statistics
... And for the text: `geom_text(position=position_jitter())` ...
written 14 months ago by ddiez1.7k
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Comment: C: Need help plotting D statistics
... For the points you can use `geom_jitter()` instead of `geom_point()` to add a small offset and avoid overlapping. ...
written 14 months ago by ddiez1.7k
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Comment: C: biomaRt getBM() returns 0 result
... What does `any(simpleCancer$chromosome == "-")` return? If `FALSE` it means none of the values in your *chromosome* column is equal to "-", and hence the result. Question: why would chromosome be equal to "-"? Are you instead looking for *strand*? ...
written 14 months ago by ddiez1.7k
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Comment: C: R unused arguments
... Please, read the [vignette][1] in the methylKit package with instructions on how to use it. You need to call `genomation::readTranscriptFeatures()`, **NOT** the deprecated function `read.transcript.features()`. [1]: https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/meth ...
written 15 months ago by ddiez1.7k
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Answer: A: R unused arguments
... Please provide, as suggested in the comments, information about your system, including what version of the package you have installed. Looking at the current version in [github][1], and as mentioned in the comments, the function `read.transcript.features()` has been deprecated. However, the replacem ...
written 15 months ago by ddiez1.7k
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Comment: C: Differential expression using microarray data and limma, where am I going wrong?
... The file is likely empty because you specified `p.value=0.01`, which means that any results with p>=0.01 will not be included. This means you probably don't have any significant changes at that level. At any rate, consider using `write.fit()`, and also, I would follow @russhh's advice on how to i ...
written 15 months ago by ddiez1.7k
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Comment: C: Defining populations in PopGenome after running readMS
... Great you found a solution! One comment: here and in your question, use the 101010 button to format chunks of code so that they look better. Take a look to other questions/answers to see the difference. ...
written 15 months ago by ddiez1.7k
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Answer: A: How calculate RPKM values for DESeq?
... You can compute rpkm from a `DESeqDataSet` in the way indicated in @igor's answer. However, RPKMs should only be used for downstream analysis and not for testing differential expression. This is explicitly mentioned in the documentation of [DEseq2][1]. >In order to test for differential expressi ...
written 15 months ago by ddiez1.7k

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