Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... Can you post a minimal working example (with all the code) to reproduce your problem, also the input data (can be "made up") and an example output file (.png, .pdf)? This is most likely the precondition for a specific and helpful reply..
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written 16 days ago by
Wolfgang Huber ♦ 13k
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... DESeqDataSetFromMatrix is not a package. There is a package called DESeq2, and its documentation is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
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written 27 days ago by
Wolfgang Huber ♦ 13k
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411
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... Btw, there is now an (even better) alternative to independent filtering: independent hypothesis weighting, IHW.
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written 6 weeks ago by
Wolfgang Huber ♦ 13k
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... Heikki
First, it'll be good to clarify concepts regarding
outlier removal: removing genes whose data do not appear to fit the mathematical model used by DESeq2 (it's called a "gamma-Poisson generalized linear model") and your design matrix
independent filtering: removing genes whose data perfec ...
written 6 weeks ago by
Wolfgang Huber ♦ 13k
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... Have a look at the IHW package, with overall variance (blind w.r.t. design factors) as a covariate. See also the accompanying paper.
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written 8 weeks ago by
Wolfgang Huber ♦ 13k
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... There's another reason to support Gordon's view. There is a fundamental difference between p-values and FDR: p-values are per-hypothesis (i.e., per-gene) properties, whereas FDR is an average across all rejected hypotheses. I.e., if you have a set of hypotheses (genes) rejected at a certain FDR $\al ...
written 8 weeks ago by
Wolfgang Huber ♦ 13k
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... Here's a few notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26
Writing papers in Rmarkdown, BiocStyle... (and books, posters)
Multi-panel figures
CRAN package multipanelfigure
Tables
knitr: kable (ideally if you then also define your own CSS); xtable ...
written 8 weeks ago by
Wolfgang Huber ♦ 13k
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467
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... Thanks, this is great!
As was asked at the Bioc-Devel Meeting, could there be support for math markdown?
E.g.
$$ \int_{-\infty}^{+\infty}f(x)\;\mathrm{d}x $$
\[ \int_{-\infty}^{+\infty}f(x)\;\mathrm{d}x \]
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written 8 weeks ago by
Wolfgang Huber ♦ 13k
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... I can reproduce this. Andrzej is away until Wednesday. It seems possible that the problem has to do with code in BiocStyle/R/auth_affil.R.
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written 9 weeks ago by
Wolfgang Huber ♦ 13k
0
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130
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... Why don't you want to update to a newer R (e.g. 3.4.1 is current)?
...
written 10 weeks ago by
Wolfgang Huber ♦ 13k
Latest awards to Wolfgang Huber
Scholar
3 months ago,
created an answer that has been accepted.
For A: Nonspecific filtering of microarray data
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
6 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Processing imaging data from high throughput compound screen with EBImage
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
17 months ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
Scholar
17 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
17 months ago,
created an answer that has been accepted.
For A: How is the mean-variance plot calculated?
Scholar
17 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
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17 months ago,
voted more than 100 times.
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar
19 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
20 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
21 months ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: rounding issues using the VSN package
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2.2 years ago,
created an answer that has been accepted.
For A: rounding issues using the VSN package
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2.3 years ago,
voted at least 25 times.
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
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3.0 years ago,
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8.2 years ago,
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