Moderator: Wolfgang Huber

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Posts by Wolfgang Huber

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Answer: A: How to Remove EBImage objects that have holes?
... There are probably better ways, but how about this: library("EBImage") x = readImage(system.file(file.path("images", "nuclei.tif"), package = "EBImage"), all = FALSE) y = thresh(x, w = 15, h = 15, offset = 0.1) yf = fillHull(y) objects = bwlabel(yf) owh = unique(objects[ y != fillHull(y) ]) obje ...
written 14 days ago by Wolfgang Huber ♦ 13k
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Answer: A: Is there a data package containing complex RNA-Seq data?
... Have a look at https://jhubiostatistics.shinyapps.io/recount/ ...
written 5 weeks ago by Wolfgang Huber ♦ 13k
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Answer: A: Errors of loading HilbertVisGUI
... Have you tried the suggestion given by the error message?   P.S.: Please also have a look at the posting guide and try to post your questions following it: https://www.bioconductor.org/help/support/posting-guide/ ...
written 11 weeks ago by Wolfgang Huber ♦ 13k
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Comment: C: rlog transformation producing outliers with very high log-transformed counts
... Two more points: Data quality: If the size factors (or indeed the library sizes) vary strongly across what should be comparable assays, is this perhaps a quality issue, meaning that some of the (presumably very low coverage) samples should be ignored rather than making a pretense of analysing the ...
written 12 weeks ago by Wolfgang Huber ♦ 13k
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... ... whereas the VST is conceptually different. It looks at the trend between variance and mean in the data, and then tries to find a strictly monotonous transformation of the data so that this trend is removed. In practice, the transformation will approach the logarithm function for high values and ...
written 3 months ago by Wolfgang Huber ♦ 13k
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Answer: A: Protein differential Expression analysis
... Julie There is no "in-principle" reason why DESeq2 shouldn't produce useful results also for count data from technologies that are not DNA-sequencing based. There are two issues: the normalization (a.k.a. size factors) the error model (Gamma-Poisson, GP) Both of these are quite generic, and w ...
written 3 months ago by Wolfgang Huber ♦ 13k
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Answer: A: Multiple tests in a single deseq object
... From how I understand your question, the answer is 'yes', Strictly speaking, you need a different object for each model fit, i.e., for each result of a call to the DESeq function with different inputs, e.g. same data but different model formula, or different arguments for the argument test. You ca ...
written 3 months ago by Wolfgang Huber ♦ 13k
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Answer: A: an unexplained phenomenon using variance stabilizing transformation for downstre
... The variance stabilizing transformation in DESeq2 is not a normalization method, it is (as the name says) a transformation. For normalization, it uses the usual DESeq2 estimateSizeFactors normalization. It is normal and expected that the results differ if you call estimateSizeFactors on the complet ...
written 4 months ago by Wolfgang Huber ♦ 13k
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Answer: A: DESeq possible when only rlog table available? (DESeq2 package)
... You need the raw counts to exactly reproduce the DESeq2 analysis. There is no easy way back from the rlog counts. You could try ordinary t-tests, linear models or limma on the rlog-data. The results should be similar (depending on data quality), but will not be the same.   ...
written 4 months ago by Wolfgang Huber ♦ 13k
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Answer: A: How is the within-subject correlation modeled in time course experiments in DESe
... Roula Have a look at the time series example in the RNA-seq workflow. There have been several threads on time courses in this forum, I encourage you to search the forum for relevant threads. E.g., https://support.bioconductor.org/p/84114/#84116 You could also opt to provide more detail on your exp ...
written 4 months ago by Wolfgang Huber ♦ 13k

Latest awards to Wolfgang Huber

Scholar 10 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 13 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 13 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: DESeq2 interacting with agricolae
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.0 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.0 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.0 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 2.0 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 2.0 years ago, voted more than 100 times.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 2.2 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.3 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.4 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.8 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 2.8 years ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 2.9 years ago, voted at least 25 times.
Scholar 3.3 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 3.6 years ago, created 100 posts.
Oracle 8.8 years ago, created more than 1,000 posts (questions + answers + comments).
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