User: henrik.seidel

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Posts by henrik.seidel

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HTqPCR does not copy featureData when subsetting a qPCRset
... When subsetting a qPCRset, the current implementation fails to transfer the featureData. Here is a fix:   diff --git a/R/qPCRset.R b/R/qPCRset.R index d400ea5..cecef29 100644 --- a/R/qPCRset.R +++ b/R/qPCRset.R @@ -73,6 +73,7 @@ function(x, i, j, drop=FALSE) { feat ...
htqpcr written 9 months ago by henrik.seidel40 • updated 9 months ago by hdvinge0
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Answer: A: Errors with HTqPCR v1.28.0 and BioC 3.4
... See https://support.bioconductor.org/p/91570/ ...
written 9 months ago by henrik.seidel40
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Answer: A: HTqPCR: bug in subsetting qPCRset
... See https://support.bioconductor.org/p/91570/ ...
written 9 months ago by henrik.seidel40
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HTqPCR cannot read more recent SDS files
... In HTqPCR, the header in SDS files is identified as the first line beginning with a hash mark (#). Newer SDS file formats use the word "Well" at the beginning of the header line instead. For that reason, HTqPCR fails to read recent SDS files. This can be solved easily by adding "Well" as one alterna ...
htqpcr written 9 months ago by henrik.seidel40 • updated 9 months ago by hdvinge0
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Answer: A: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... I think I solved both issues now. I removed the "validate" argument from the calls to assayDataElementReplace. When subsetting a qPCRset, there was a call to the function "unname" before assigning the subset of the original exprs to the new qPCRset: exprs=unname(exprs(x)[i, j, drop=FALSE]) It ...
written 9 months ago by henrik.seidel40
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Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Patch removed, see answer. ...
written 9 months ago by henrik.seidel40
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Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Okay, the patch below makes it at least possible to assign modified expression sets to a qPCRset (so I can at least fix the sample names). But subsetting a qPCRset still removed sample names. So there seems to be more which requires a fix. ...
written 9 months ago by henrik.seidel40
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Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Just saw that you used "validate=FALSE" for "featureCategory" and "flag", so removing the "validate" argument would change something for older Bioconductor versions. Not sure if this would be an issue. ...
written 9 months ago by henrik.seidel40
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Subsetting qPCRset loses sample names, possibly due to change of assayDataElementReplace
... When subsetting a qPCRset (e.g., for features), the sample names get lost. Assigning an expression set explicitly does not work as well. Let's say raw is a qPCRset: rawSub <- raw[myFeatures, ] sampleNames(raw) # result is correct, e.g. "Sample1", "Sample2", ... sampleNames(rawSub) # result is ...
htqpcr written 9 months ago by henrik.seidel40
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Comment: C: DESeq2: Possible issue with colData and sorting
... Thank you Martin, and thanks to all of you for your comments. ...
written 14 months ago by henrik.seidel40

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