User: Casper Peters

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Posts by Casper Peters

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Comment: C: [DEVELOPMENT] Trying to use development version of Bioconductor, needs R 3.6?...
... 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. ...
written 5 months ago by Casper Peters0
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Comment: C: [DEVELOPMENT] Trying to use development version of Bioconductor, needs R 3.6?...
... Alright, thanks :) ...
written 5 months ago by Casper Peters0
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[DEVELOPMENT] Trying to use development version of Bioconductor, needs R 3.6?...
... 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 ...
bioc-devel developers written 5 months ago by Casper Peters0
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Comment: C: unable to find an inherited method for function counts for signature DESeqTransf
... 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.)   ...
written 18 months ago by Casper Peters0
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Comment: C: unable to find an inherited method for function counts for signature DESeqTransf
... 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 18 months ago by Casper Peters0
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Comment: A: unable to find an inherited method for function counts for signature DESeqTransf
... I already tried validating my install with biocValid(), my session is valid. ...
written 18 months ago by Casper Peters0
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unable to find an inherited method for function counts for signature DESeqTransform
... 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) ...
deseq2 counts variance deseqtransform deviation written 18 months ago by Casper Peters0 • updated 18 months ago by Michael Love23k

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