User: henrik.seidel

gravatar for henrik.seidel
Reputation:
40
Status:
New User
Location:
Last seen:
1 year, 4 months ago
Joined:
1 year, 10 months ago
Email:
h************@bayer.com

Posts by henrik.seidel

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
392
views
1
answer
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 17 months ago by henrik.seidel40 • updated 17 months ago by hdvinge0
0
votes
1
answers
603
views
1
answers
Answer: A: Errors with HTqPCR v1.28.0 and BioC 3.4
... See https://support.bioconductor.org/p/91570/ ...
written 17 months ago by henrik.seidel40
0
votes
1
answers
395
views
1
answers
Answer: A: HTqPCR: bug in subsetting qPCRset
... See https://support.bioconductor.org/p/91570/ ...
written 17 months ago by henrik.seidel40
0
votes
1
answer
323
views
1
answer
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 17 months ago by henrik.seidel40 • updated 17 months ago by hdvinge0
0
votes
1
answers
511
views
1
answers
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 17 months ago by henrik.seidel40
0
votes
1
answers
511
views
1
answers
Comment: C: Subsetting qPCRset loses sample names, possibly due to change of assayDataElemen
... Patch removed, see answer. ...
written 17 months ago by henrik.seidel40
0
votes
1
answers
511
views
1
answers
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 17 months ago by henrik.seidel40
0
votes
1
answers
511
views
1
answers
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 17 months ago by henrik.seidel40
3
votes
1
answer
511
views
1
answer
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 17 months ago by henrik.seidel40
0
votes
3
answers
597
views
3
answers
Comment: C: DESeq2: Possible issue with colData and sorting
... Thank you Martin, and thanks to all of you for your comments. ...
written 22 months ago by henrik.seidel40

Latest awards to henrik.seidel

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 218 users visited in the last hour