Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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- Joined:
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Posts by Wolfgang Huber
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... You say "i was not succesful" but not really what you consider your problem is...
However, I'd recommend taking a much better approach, namely use Rmarkdown (or knitr) to prepare your analysis script, and use PDF as the output format.
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written 7 days ago by
Wolfgang Huber ♦ 13k
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95
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... Can you please post
a (minimal) code example
make sure you use recent package versions, and provide the output of devtools::session_info() ?
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written 7 days ago by
Wolfgang Huber ♦ 13k
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... See also R FAQ 7.31 https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f
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written 10 days ago by
Wolfgang Huber ♦ 13k
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... I don't think I know all the different varieties of MS data, but for many quantitative MS data types, it is appropriate to treat them as continuous measurements on which you can use ordinary statistical models and tests, possibly with empirical Bayes moderation (limma) and/or suitable transformation ...
written 20 days ago by
Wolfgang Huber ♦ 13k
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96
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... Why do you think that? "need" is a strong term, but filtering (or weighting, see my reply below) can improve an analysis by giving better power.
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written 20 days ago by
Wolfgang Huber ♦ 13k
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... In many cases, using data-driven weights for the multiple testing computation is a better approach than yes/no filtering, see e.g. the IHW vignette and the associated paper. The vignette also gives hints on the choice of the weighting covariate and diagnostic plots.
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written 20 days ago by
Wolfgang Huber ♦ 13k
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110
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Answer:
A: AIC-like measure for DESeq2
... You could use cross-validation: fit the model on a subset of the samples, then apply to the held-out samples and show that prediction performance on these increases.
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written 6 weeks ago by
Wolfgang Huber ♦ 13k
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113
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... It appears that your dataset does not yield any evidence for differential expression. So you could use the same data, but make a different comparison, or use a new dataset and make the same comparison.
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written 8 weeks ago by
Wolfgang Huber ♦ 13k
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131
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... Did you try with using the assignment operator "<-" instead of the comparison "<" in your command line?
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written 8 weeks ago by
Wolfgang Huber ♦ 13k
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185
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... Also the curatedMetagenomicData package, http://bioconductor.org/packages/devel/data/experiment/html/curatedMetagenomicData.html
...
written 9 weeks ago by
Wolfgang Huber ♦ 13k
Latest awards to Wolfgang Huber
Scholar
15 days ago,
created an answer that has been accepted.
For A: Nonspecific filtering of microarray data
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
3 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Processing imaging data from high throughput compound screen with EBImage
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
14 months ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
Scholar
14 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
14 months ago,
created an answer that has been accepted.
For A: How is the mean-variance plot calculated?
Scholar
14 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Voter
14 months ago,
voted more than 100 times.
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar
16 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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
18 months ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
Scholar
23 months ago,
created an answer that has been accepted.
For A: rounding issues using the VSN package
Scholar
23 months ago,
created an answer that has been accepted.
For A: rounding issues using the VSN package
Supporter
2.1 years ago,
voted at least 25 times.
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion
2.8 years ago,
created 100 posts.
Oracle
7.9 years ago,
created more than 1,000 posts (questions + answers + comments).
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