Moderator: Kasper Daniel Hansen

Reputation:
6,380
Status:
Trusted
Location:
United States
Website:
http://www.hansenlab.org/
Twitter:
KasperDHansen
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
13 years, 1 month ago
Email:
k*****************@gmail.com

Posts by Kasper Daniel Hansen

<prev • 711 results • page 2 of 72 • next >
0
votes
1
answers
188
views
1
answers
Answer: A: IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
... The number of probes inside an IDAT file depends on the settings of the scanner at the time of the scanning of the file. This is encaptured in a so-called DMAP file. Unfortunately, Illumina has releaed multiple DMAP files for the EPIC chip so it is quite standard to see what you see. This was never ...
written 8 months ago by Kasper Daniel Hansen6.4k
0
votes
2
answers
450
views
2
answers
Comment: C: Error using read.metharray.exp in minfi to read idat files
... Suggestion on how to make all of this more robust would be great; happy to make more checks. Perhaps file an issue on GitHub. On Wed, Oct 25, 2017 at 7:20 AM, Andy91 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User ...
written 11 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answers
884
views
1
answers
Comment: C: minfi - estimatecellcount function
... What is the output of annotation(rgSet_blood) sessionInfo() (last one after the error). When did you create this rgSet - a long time ago, recently or just now? Best, Kasper On Wed, Oct 25, 2017 at 6:12 AM, poojitha.stemcell [bioc] < noreply@bioconductor.org> wrote: > Activity on a ...
written 11 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answers
356
views
1
answers
Comment: C: BSmooth 'names' attribute must be the same length as the vector
... your zero-coverage sounds weird. On Tue, Oct 24, 2017 at 10:34 PM, ravi.tharakan [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User ravi.tharakan <https: support.bioconductor.org="" u="" 14221=""/> wrote Comm ...
written 11 months ago by Kasper Daniel Hansen6.4k
0
votes
2
answers
573
views
2
answers
Comment: C: Is it possible to convert Methylumi object into RGChannelSet
... Its the same issue. When you get intensities only from GEO you do not get   - control probes   - out of band probes To get this information, you generally need the original IDAT files. This means that any algorithm which makes use of either control probes or out of band probes will fail. ...
written 11 months ago by Kasper Daniel Hansen6.4k
0
votes
0
answers
745
views
0
answers
Comment: C: Rgraphviz installation fails
... You should do # env | grep usr/lib to see what is being set. You could also try to have a look at # R CMD config CFLAGS # R CMD config LDFLAGS Comparing to the build report, which has the following invocation: /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module -avoid-version ...
written 13 months ago by Kasper Daniel Hansen6.4k
0
votes
0
answers
745
views
0
answers
Comment: C: Rgraphviz installation fails
... You're using the bundled Graphviz, so the fact you have it installed in your system shouldn't matter. This looks weird: /bin/bash ./libtool --tag=CC --mode=link gcc -std=gnu99 -g -O2 -module -avoid-version -L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl -o dlopen.la dlopen. ...
written 13 months ago by Kasper Daniel Hansen6.4k
0
votes
0
answers
745
views
0
answers
Comment: C: Rgraphviz installation fails
... You don't need to install Graphviz yourself, it is bundled with Rgraphviz. What is the beginning of the Rgraphviz installation output and what command (exactly) do you use to install it? ...
written 13 months ago by Kasper Daniel Hansen6.4k
0
votes
3
answers
689
views
3
answers
Comment: C: ChAMP filter removing good samples from different batch of EPIC arrays.
... The many failed samples is because the data from these (later) arrays are scrambled and therefore garbage. This happens when you read epic arrays which have different number of probes in, with earlier versions of minfi. This is fixed in current release. Best, Kasper (Sent from my phone.) > On A ...
written 13 months ago by Kasper Daniel Hansen6.4k
0
votes
1
answers
364
views
1
answers
Answer: A: minfi - error when reading idat files
... This looks good to me. You don't get an error with force=TRUE. What you're seeing is that you have two sets of IDAT files scanned with different scan settings (specifically with different DMAP files). We see this a lot with the EPIC array. It is unfortunate that Illumina has released some many D ...
written 14 months ago by Kasper Daniel Hansen6.4k

Latest awards to Kasper Daniel Hansen

Popular Question 21 months ago, created a question with more than 1,000 views. For Views on BSgenome object
Popular Question 21 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 21 months ago, created a question with more than 1,000 views. For defaults in BiocParallel
Scholar 2.4 years ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 2.4 years ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet 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 3.0 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Appreciated 3.0 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Scholar 3.8 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 8.6 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 150 users visited in the last hour