Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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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 18 days ago by
Wolfgang Huber ♦ 13k
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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 4 weeks ago by
Wolfgang Huber ♦ 13k
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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 4 weeks ago by
Wolfgang Huber ♦ 13k
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... Also the curatedMetagenomicData package, http://bioconductor.org/packages/devel/data/experiment/html/curatedMetagenomicData.html
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written 5 weeks ago by
Wolfgang Huber ♦ 13k
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... Not too large, but too different from what DESeq2 expects.
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written 5 weeks ago by
Wolfgang Huber ♦ 13k
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... Can you do some exploratory data analysis (EDA) & visualisation to see how the mean-variance relationship of your data looks like?
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written 5 weeks ago by
Wolfgang Huber ♦ 13k
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... In addition to Mike's answer, let me add, as a more general comment, that it is always helpful to distinguish between the route taken and the destination, i.e., between the assumptions made to come up with an algorithm for finding a data transformation, and the usefulness of the transformation that ...
written 5 weeks ago by
Wolfgang Huber ♦ 13k
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... ... and also https://www.bioconductor.org/help/workflows/rnaseqGene/
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written 6 weeks ago by
Wolfgang Huber ♦ 13k
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... gcrma is a sophisticated and numerically somewhat complex algorithm; it is possible that ties might be induced as you describe.
I'd recommend:
Trying with plain rma
Plotting the data from some of the offending probe set at the per-probe level, e.g. as in Fig.12 of Chapter 3 of the Case Studies ...
written 7 weeks ago by
Wolfgang Huber ♦ 13k
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... Can you talk to the people who went to the expense and effort to create this data set to find out what the objective of creating it was?
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written 7 weeks ago by
Wolfgang Huber ♦ 13k
Latest awards to Wolfgang Huber
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Processing imaging data from high throughput compound screen with EBImage
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: package specifically dedicated to a manuscript
Scholar
13 months ago,
created an answer that has been accepted.
For A: plotMA for unshrunken LFC in deseq2
Scholar
13 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar
13 months ago,
created an answer that has been accepted.
For A: How is the mean-variance plot calculated?
Scholar
13 months ago,
created an answer that has been accepted.
For A: DESeq2 interacting with agricolae
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13 months ago,
voted more than 100 times.
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar
15 months ago,
created an answer that has been accepted.
For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
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: plotMA for unshrunken LFC in deseq2
Scholar
22 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
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2.0 years ago,
voted at least 25 times.
Scholar
2.4 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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2.7 years ago,
created 100 posts.
Oracle
7.9 years ago,
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