Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.4k
- Reputation:
- 6,440
- Status:
- Trusted
- Location:
- United States
- Website:
- http://www.hansenlab.org/
- Twitter:
- KasperDHansen
- Scholar ID:
- Google Scholar Page
- Last seen:
- 7 months, 4 weeks ago
- Joined:
- 14 years, 1 month ago
- Email:
- k*****************@gmail.com
Posts by Kasper Daniel Hansen
<prev
• 723 results •
page 1 of 73 •
next >
0
votes
1
answer
55
views
1
answers
... In minfi we have the function subsetByLoci() which might be useful in these
situations. The issue is that an RGChannelSet is indexed by Addresses (kind
of locations of the probes) while a MethylSet (and friends) is indexed by
CpG names and we sometimes have multiple addresses <-> 1 CpG because ...
written 6 weeks ago by
Kasper Daniel Hansen ♦ 6.4k
0
votes
1
answer
113
views
1
answers
... If you send me the input, I can take a slow look.
Best,
Kasper
(Sent from my phone.) ...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.4k
0
votes
1
answer
90
views
1
answers
... If these are indeed the same arrays, but just with slightly different
number of beads, then it should work. If not, then it shouldn't (Ie you
cannot read in 450k and EPIC together). It is hard to know which case it
is. If you want more help, you should make (some of) the idat files
available on drop ...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.4k
1
vote
2
answers
143
views
2
answers
... Just reading over the code, I am guessing that RCy3 has a problem with
subgraphs? ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
1
vote
1
answer
129
views
1
answers
Answer:
A: mini error in read.metharray
... If you're using read.metharray, the base names argument is a vector which
is half the length of the number of files, equal to the number of samples.
You need to remove the _Grn and _Red from the file names and remove any
duplicates.
read.metharray.exp() is probably an easier to use interface. ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
0
votes
1
answer
150
views
1
answers
... 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 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
1
vote
1
answer
150
views
1
answers
... What is the output of
summary(GC_content[,1])
Best,
Kasper ...
written 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
2
votes
2
answers
187
views
2
answers
... 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 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
0
votes
2
answers
225
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 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
0
votes
0
answers
256
views
0
answers
... 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 10 months ago by
Kasper Daniel Hansen ♦ 6.4k
• updated
10 months ago by
Martin Morgan ♦♦ 23k
Latest awards to Kasper Daniel Hansen
Popular Question
7 months ago,
created a question with more than 1,000 views.
For smoothing function in bumphunter in minfi
Great Question
10 months ago,
created a question with more than 5,000 views.
For Bioconductor on Coursera
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Bioconductor on Coursera
Popular Question
10 months ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Popular Question
10 months ago,
created a question with more than 1,000 views.
For using offsets from EDASeq and cqn for edgeR
Scholar
10 months ago,
created an answer that has been accepted.
For A: Illumina Methylation 27k minfi
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Views on BSgenome object
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For defaults in BiocParallel
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: Minfi User Guide Build Problem?
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: Covert MethylSet to RGChannelSet object
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: Minfi RGChannelSet preprocessing error in assayDataElement
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For Bioconductor on Coursera
Scholar
4.9 years ago,
created an answer that has been accepted.
For A: QC/normalization standards for cancer studies with 450k array data
Centurion
9.7 years ago,
created 100 posts.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 269 users visited in the last hour