User: Keith Hughitt

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Keith Hughitt120
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Posts by Keith Hughitt

<prev • 54 results • page 1 of 6 • next >
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Comment: C: rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
... Good call. I ran into the same issue, and after trying `base::rowSums()` with no success, was left clueless. I wonder if perhaps Bioconductor should be updated so-as to better detect sparse matrices and call the appropriate function? The current error message is not very informative. ...
written 5 months ago by Keith Hughitt120
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Comment: C: Unexpected format to the list of available marts error (12/11/2017)
... I can confirm the present server issues. Below, for example, the first two requests below succeed and the later two fail: > useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org') Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the ...
written 12 months ago by Keith Hughitt120
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Answer: A: Finding orthologous human/mouse ENSEMBL IDs
... In case it helps anyone else, I was able to solve this using the second method suggested in the earlier post -- biomaRt's "getLDS()" function: mart1 = useMart("ensembl", dataset="hsapiens_gene_ensembl") mart2 = useMart("ensembl", dataset="mmusculus_gene_ensembl") human_ids <- c('E ...
written 18 months ago by Keith Hughitt120
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Finding orthologous human/mouse ENSEMBL IDs
... Greetings, I was wondering if someone might be able to help suggest a good way to generate a mapping of human/mouse orthologs, using ENSEMBL gene IDs? I found a very old post which pointed me to the inpIDMapper function in the AnntoationDbi package. The example usage shows how this function can be ...
annotationdbi ensembl human mouse homologue written 18 months ago by Keith Hughitt120
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Comment: C: rtracklayer import.gff3 function no longer working in R 3.4
... Indeed it does! downgrade with biocLite(c("ExpressionAtlas", "GenomeInfoDb", "OrganismDbi", "knitcitations")) Error: 288 package(s) out of date; 4 package(s) too new In the past, I would just use "biocLite()" to see which packages were out-of-date, but that was not returning anything in this c ...
written 19 months ago by Keith Hughitt120
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Comment: C: rtracklayer import.gff3 function no longer working in R 3.4
... Good catch! It looks like the "3.4" directory may have been previously used by the SVN version of of R, and some newer packages got mixed in. Martin's suggestion below further supports this. Thanks for the insight! ...
written 19 months ago by Keith Hughitt120
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rtracklayer import.gff3 function no longer working in R 3.4
... After upgrading to R 3.4/Bioconductor 3.4 today, the `import.gff3` function (and presumably other related functions) are no longer working for me. For example, using this sample GFF3 file from ENSEMBL, with spaces replaced with tabs: ##gff-version 3 ctg123 . mRNA 1300 9000 . ...
rtracklayer gff import.gff3 written 19 months ago by Keith Hughitt120 • updated 19 months ago by Martin Morgan ♦♦ 22k
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Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
... Greetings, I'm currently working on a pipeline which makes use of the downloadable version of the covariance model-based RNA motif detection program, CMFinder. CMFinder outputs detected motifs in a modified version of the Stockholm output format. (Example: http://bio.cs.washington.edu/CMfinder/glm ...
biostrings msa stockholm cmfinder written 23 months ago by Keith Hughitt120
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Comment: C: ArrayExpress unable to find raw data: "Experiment has no raw files available"
... Thanks for the clarification, Ugis. Do you know why that is the case, of if it is stated anywhere? I did not see any note in the package vignette / manual regarding lack of support for RNA-Seq data. ...
written 2.0 years ago by Keith Hughitt120
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ArrayExpress unable to find raw data: "Experiment has no raw files available"
... Hello, I just tried using the ArrayExpress library for the first time to retrieve some RNA-Seq samples through the EBI ArrayExpress database. When I attempt to call the ArrayExpress function, however, I run into the following error: > library(ArrayExpress) ...
arrayexpress written 2.0 years ago by Keith Hughitt120 • updated 2.0 years ago by ugis10

Latest awards to Keith Hughitt

Popular Question 3 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Student 18 months ago, asked a question with at least 3 up-votes. For WGCNA: overlapping colors in plotDendroAndColors?
Voter 18 months ago, voted more than 100 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 23 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For WGCNA: overlapping colors in plotDendroAndColors?
Supporter 3.5 years ago, voted at least 25 times.

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