User: Casper Peters
Casper Peters • 0
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Posts by Casper Peters
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... I am using Ubuntu 16.04 Desktop. I will be sure to ask the bioc-devel mailing instead :). Can you maybe point towards the devel binaries of 3.6? I can't seen to find this anywhere. If they don't exist, I'll still have to try fix my compilation.
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written 7 months ago by
Casper Peters • 0
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... Alright, thanks :)
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written 7 months ago by
Casper Peters • 0
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... So I am trying to make a package for Bioconductor, but I have to use the latest Bioc-devel. When I tried installing this, it told me I'd need R 3.6? R 3.6 has not been released yet and is a development stage. I tried compiling the latest R devel version but am having issues. Mainly getting the follo ...
written 7 months ago by
Casper Peters • 0
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... Maybe you got an error calling counts() on a DESeqTransform object?
This. I didn't see I used the wrong variable there. We have a saying in dutch; "I can't see the forest through all the trees." We use it when we're being too short-sighted / get confused because of clusterfucks (like my code.)
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written 20 months ago by
Casper Peters • 0
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... Running the class and typeof command returns the following (my variable has a different name);
> class(cds)
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
> typeof(cds)
[1] "S4"
So, seeing the output, I don't think I have a wrong object that I'm putting in.
However, looking at ntd (nds ...
written 20 months ago by
Casper Peters • 0
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... I already tried validating my install with
biocValid(), my session is valid.
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written 20 months ago by
Casper Peters • 0
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... I have a problem in regards to making a variance plot from our data. I tried to use a code snippet from here (Effects of transformations on the variance): https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
when trying the code snippet;
# this gives log2(n + 1)
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written 20 months ago by
Casper Peters • 0
• updated
20 months ago by
Michael Love ♦ 24k
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