User: james
james • 20
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Posts by james
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... As @MatthewP observed, the new version of AnnotationDbi is dropping a few hundred UNIPROTs.
Just guessing, but is AnnotationDbi keeping a list of "stale" UNIPROTs? ...
written 13 days ago by
james • 20
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... Exactly 361 more UNIPROTs with the older version of AnnotationDbi, i.e. the new version gives a subset of the old version. ...
written 13 days ago by
james • 20
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... Sorry, but it sounds like you don't know the answer to my question?
One has a few hundred more UNIPROTs than the other. ...
written 13 days ago by
james • 20
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... OK, but as explained in my question, I don't see why anything besides the hgu219.db version is relevant.
Computer 1:
> R.Version()$version.string
[1] "R version 3.6.3 (2020-02-29)"
> library(BiocManager)
Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install f ...
written 14 days ago by
james • 20
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... Yes, of course. This is exactly what I did. On both systems:
> packageVersion('hgu219.db')
[1] ‘3.2.3’ ...
written 14 days ago by
james • 20
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... I thought that all of the information about each chipset (i.e. platform) was in the corresponding R package.
For example, hgu219.db is the annotation package for the hgu219 platform.
However, my key lookup results differ depending on the package version of AnnotationDbi, even when the hgu219.db pa ...
written 14 days ago by
james • 20
• updated
13 days ago by
benformatics • 2.0k
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... Ah, thank you. I didn't read the original answer carefully enough.
Unfortunately, the program I am trying to use: https://github.com/kiharalab/DOVE, exits with an error depending on what is after the z-coordinate. I will look into the code to try and determine whether it actually relies on the inf ...
written 5 months ago by
james • 20
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... Sorry for the late reply. I thought I would be notified by email if anyone responded.
The problem is that in the example I gave, the fields do not match the ATOM specification. They only approximately correspond. Here is what a pdb file downloaded with pdb-tools looks like. It matches the ATOM spec ...
written 6 months ago by
james • 20
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... I am new to working with PDB format files, and I am having difficulty working with the ZDOCK Benchmark files.
Their input PDBs for generating decoys seem to have 2 extra columns, and the filenames end with *.pdb.ms
Does anyone know what type of files these really are?
The output decoy PDBs gene ...
written 6 months ago by
james • 20
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... I am helping prepare data downloaded from ArrayExpress to be used in a machine learning algorithm.
The algorithm expects one sequence of gene expression values for each UNIPROT. However, the data is organized (as usual I assume, but I am new to this area) so that there is one sequence of gene expr ...
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