Moderator: Kasper Daniel Hansen

Reputation:
6,410
Status:
Trusted
Location:
United States
Website:
http://www.hansenlab.org/
Twitter:
KasperDHansen
Scholar ID:
Google Scholar Page
Last seen:
2 months ago
Joined:
13 years, 8 months ago
Email:
k*****************@gmail.com

Posts by Kasper Daniel Hansen

<prev • 718 results • page 1 of 72 • next >
0
votes
1
answer
63
views
1
answers
Comment: C: Error using Conditional Quartile Normalization (CQN)
... Well, it shows that you do in fact have NA's in the length vector, contrary to what you said. You could remove those 25 genes or figure out what their length is and enter it into the GC_content object. Best, Kasper ...
written 6 weeks ago by Kasper Daniel Hansen6.4k
1
vote
1
answer
63
views
1
answers
Answer: A: Error using Conditional Quartile Normalization (CQN)
... What is the output of summary(GC_content[,1]) Best, Kasper ...
written 6 weeks ago by Kasper Daniel Hansen6.4k
2
votes
2
answers
94
views
2
answers
Answer: A: Illumina Methylation 27k minfi
... This bug is fixed in minfi 1.29.4 (devel) and 1.28.4 (release) which I have just committed. Assuming they build fine, they will be available in a few days from Bioconductor and immediately from the GitHub page. Thanks for the report and the diagnose. Best, Kasper ...
written 6 weeks ago by Kasper Daniel Hansen6.4k
0
votes
2
answers
132
views
2
answers
Comment: C: Reading 450k data in minfi
... The content you posted is the array design, not the actually measurements. You should not have to read this file in. ...
written 6 weeks ago by Kasper Daniel Hansen6.4k
0
votes
0
answers
158
views
0
answers
Comment: C: Rgraphviz installation from source on Linux (Fedora 28) w BioC 3.8 -- failure
... This is a very weird error (missing XXX_pow_finite). We have confirmed that this arises when you use -O3 optimization which GCC 8 (or newer). The solution to this issue is to downgrade the optimization. The solution I intent to implemented (but slipped off my todo list) is to modify the configure sc ...
written 4 months ago by Kasper Daniel Hansen6.4k • updated 4 months ago by Martin Morgan ♦♦ 23k
0
votes
0
answers
203
views
0
answers
Comment: C: Rgraphviz installation fails in R with OpenBLAS
... Peter, I took a more careful look at your report. Are the two different R installations (with and without OpenBLAS) compiled with different compilers?  I know that Rgraphviz fails using GCC 8 with -O3 optimization flags, with this particular error (missing `***__pow_finite`). You don't mention in y ...
written 4 months ago by Kasper Daniel Hansen6.4k
0
votes
0
answers
203
views
0
answers
Comment: C: Rgraphviz installation fails in R with OpenBLAS
... First a clarification. Version 2.26 is the Rgraphviz version 2.28 is the Graphviz versioon they have nothing to do with each other, although now that 26 ~ 28 it looks weird. Second, I figured out what the issue is, but I dropped the ball in fixing it. On Wed, Nov 28, 2018 at 9:45 AM mmokrejs [ ...
written 4 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answer
216
views
1
answers
Answer: A: Taking relatedness among individuals into account in differential methylation an
... At first, I would use "standard" tools from GWAS to do this (not saying this is easy), either on data in the unit interval or the logit transformation. In principle all you need is a mixed effect model where the covariance matrix reflects the relatedness structure. On Sat, Aug 25, 2018 at 12:34 AM ...
written 8 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answer
203
views
1
answers
Comment: C: annotationhub: data update
... In this case, this is an interface to a UCSC resource which I believe is provided by the core team (I could be wrong though). The implications (to me) is that as time goes on, the AnnotationHub version of the resource deviates from UCSC. I understand short term deviations in the sense that UCSC ha ...
written 8 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answer
203
views
1
answer
annotationhub: data update
... If I run the following code to get RefSeq from UCSC: library(AnnotationHub) ahub <- AnnotationHub() ahub <- subset(ahub, species == "Homo sapiens" & genome == "hg19") query(ahub, "refseq")[1] I see > query(ahub, "refseq")[1] AnnotationHub with 1 record # snapshotDate(): 2018-08-01 ...
annotationhub written 8 months ago by Kasper Daniel Hansen6.4k • updated 8 months ago by shepherl ♦♦ 1.3k

Latest awards to Kasper Daniel Hansen

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Views on BSgenome object
Popular Question 2.4 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 2.4 years ago, created a question with more than 1,000 views. For defaults in BiocParallel
Scholar 3.0 years ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 3.0 years ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Popular Question 3.0 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Appreciated 3.6 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Scholar 4.4 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 9.2 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 165 users visited in the last hour