User: james

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james20
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Posts by james

<prev • 10 results • page 1 of 1 • next >
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Comment: C: key lookup changes with AnnotationDbi version
... 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 james20
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Comment: C: key lookup changes with AnnotationDbi version
... 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 james20
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Comment: C: key lookup changes with AnnotationDbi version
... 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 james20
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Comment: C: key lookup changes with AnnotationDbi version
... 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 james20
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Comment: C: key lookup changes with AnnotationDbi version
... Yes, of course. This is exactly what I did. On both systems: > packageVersion('hgu219.db') [1] ‘3.2.3’ ...
written 14 days ago by james20
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key lookup changes with AnnotationDbi version
... 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 ...
R bioconductor written 14 days ago by james20 • updated 13 days ago by benformatics2.0k
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Comment: A: ZDOCK Benchmark PDB files have unusual format
... 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 james20
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Comment: A: ZDOCK Benchmark PDB files have unusual format
... 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 james20
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ZDOCK Benchmark PDB files have unusual format
... 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 ...
next-gen written 6 months ago by james20
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How to amalgamate gene expressions grouped by UNIPROT?
... 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 ...
sequencing written 15 months ago by james20 • updated 13 months ago by Biostar ♦♦ 20

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