User: Bernd Klaus
Bernd Klaus • 560
- Reputation:
- 560
- Status:
- Trusted
- Location:
- Germany
- Twitter:
- @BKlausStats
- Last seen:
- 11 months, 4 weeks ago
- Joined:
- 5 years, 10 months ago
- Email:
- b**********@embl.de
Posts by Bernd Klaus
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... Hello,
thanks a lot for your very detailed post!
As you noted yourself, the parametric fit seems to slightly overestimate the dispersions for your data, so the p-values you get from the Wald test z-scores are too large on average, fdrtool re-estimates the variance of the z-scores and gives you a ...
written 12 months ago by
Bernd Klaus • 560
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... You can also try to compare the dispersion estimates for the different time points directly as the prior comparison assumes that the trend fit is similar (I edited my answer accordingly). They can be accessed via rowData(dds)$dispersion. And you could e.g. look at a scatterplot of log10(rowData(dds) ...
written 23 months ago by
Bernd Klaus • 560
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... Hi Ronald,
as Mike said, there is always some "detective work" involved on determining why a p-value distribution doesn't look like it "should".
In my workflow, I validated the correction by looking at the overlap of the results of the original analysis with my corrected list, where I find 105 ...
written 23 months ago by
Bernd Klaus • 560
0
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... I agree with Gavins's answer - the code will exclude all probe IDs with multiple mappings to gene symbols, so by definition there should not be any duplicate PROBEIDs in fData as I retain only the PROBEIDs matching to exactly one gene symbol.
Are you using the correct annotation database for your a ...
written 2.0 years ago by
Bernd Klaus • 560
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...
The team will update the function. In the meantime you can simply use my function https_getAE in the the github gist linked to above in order to make it work again.
...
written 2.0 years ago by
Bernd Klaus • 560
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... Dear ArrayExpress development team,
EBI services (<https://www.ebi.ac.uk/services>), including ArrayExpress have switched to https on October 1st 2017. The function getAE from the ArrayExpress Bioconductor package needs an update, as any retrieval fails like so:
library(ArrayExpress)
getA ...
written 2.0 years ago by
Bernd Klaus • 560
• updated
2.0 years ago by
Wolfgang Huber ♦ 13k
1
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1.3k
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... Hi Thyago,
The PCA plot looks pretty much like a batch effect being a stronger "separator" than the experimental groups.
You should tackle this directly. After application of fdrtool, you move to a rather bathtub shaped p-value histogram which often indicates p-values that are too liberal (you ...
written 2.1 years ago by
Bernd Klaus • 560
0
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... if you are interested in two group comparisons only, the st CRAN package implements various alternative variance shrinkage estimators, the CAT score even takes correlations between the genes into account:
http://strimmerlab.org/software/st/index.html
...
written 2.4 years ago by
Bernd Klaus • 560
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... If you are sure that there are no batch effects, try to run a stronger prefiltering of your data, e.g.
rowSums(counts(dds)) > 20
or something like that since you had spikes near 1 in the p-value histograms you sent to my by mail. The fdrtool results cannot directly indicate whether there is ...
written 2.6 years ago by
Bernd Klaus • 560
0
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... As Mike said, this is a quite subjective decision. If the p-value is hill shaped, the p-values are on avarage "higher than expected" leading to a potentially to a lower power.
However, Wolfgang pointed me to the fact that these histogram shapes can result from batch effects in your data that overla ...
written 2.6 years ago by
Bernd Klaus • 560
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