Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.4k
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- http://www.hansenlab.org/
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- Last seen:
- 9 months, 4 weeks ago
- Joined:
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Posts by Kasper Daniel Hansen
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... 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 3 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... If you send me the input, I can take a slow look.
Best,
Kasper
(Sent from my phone.) ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... 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 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... Just reading over the code, I am guessing that RCy3 has a problem with
subgraphs? ...
written 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
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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 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
0
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... 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 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
1
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1
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184
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... What is the output of
summary(GC_content[,1])
Best,
Kasper ...
written 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
2
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213
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... 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 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
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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 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... 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 12 months ago by
Kasper Daniel Hansen ♦ 6.4k
• updated
12 months ago by
Martin Morgan ♦♦ 24k
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