Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Comment: C: Cannot load CEL files
... does file.exists("~/Downloads/GSE17204_RAW/GSM430339.CEL") yield TRUE? ...
written 13 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs
... This was cross-posted to bioc-devel.  The answer that I provided there was: You can get the information through the merged tables: > dbListTables(con) [1] "gds" "gds_subset" "geoConvert" [4] "geodb_column_desc" "gpl" "gse" [7] "gse_gpl ...
written 14 months ago by Vincent J. Carey, Jr.6.2k • updated 14 months ago by Sean Davis21k
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Answer: A: how to find Snps that are within 1e6 from gene
... You should structure the location data you've provided as GRanges instance. if your gene data are available in a data.frame as e.g.,  > genes geneName chrom txStart txEnd 1 A1BG chr19 58858171 58864865 2 A1BG-AS1 chr19 58863335 58866549 3 A1CF chr10 52559168 52645435 ...
written 17 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Mapping regions to gene symbols
... look for the difference between seqinfo(mygr) and seqinfo(r2syms) seqlevelsStyle(mygr) and seqlevelsStyle(r2syms) get them to coincide. it can take some work. simplest is often seqlevelsStyle(mygr) = seqlevelsStyle(r2syms) assuming GenomeInfoDb package is attached On Sat, Jul 1, 2017 at 3:2 ...
written 17 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: Mapping regions to gene symbols
... For all its apparent simplicity, this question is not very clear.  One warning sign is: seqinfo: 23 sequences from an unspecified genome; no seqlengths How are we supposed to know what reference genome defines the genomic coordinates?  This is essential information for mapping between characteris ...
written 17 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: No annotation for single SNPs
... i'd say the clue is to look at the output of AllVariants() maybe Val can comment further on how to increase scope On Wed, Jun 21, 2017 at 7:48 AM Lna [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Lna <htt ...
written 18 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: No annotation for single SNPs
... "according to the UCSC the SNP is part of an intron" -- but you have used AllVariants(promoter=PromoterVariants(downstream=500))) in your locateVariants() call.  Try IntronVariants().  I would not be surprised if there were still some mismatches -- please provide full details if identified, it i ...
written 18 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Using AMI with StarCluster - error authenticating
... We are finding that cfncluster creation of clusters in EC2 is extremely slow, relative to the solution available a few years through starcluster.  Any other approaches in use in our community? ...
written 21 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
... I don't know that SummarizedExperiment is a good target for what you are trying to do. Is there a matrix of values to serve as "assay", with rows corresponding to features and columns corresponding to samples? Organizing such a matrix in coordination with feature-level and sample-level and experime ...
written 21 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
...   Briefly, there is no simple approach to this.  However, to get a working example: library(GenomicRanges) library(SummarizedExperiment) example(GRangesList) # creates 'grl' in .GlobalEnv colrep = function(x,n) matrix(x, nr=length(x), nc=n) # utility to create usable 'assay' msel = lapply(grl, ...
written 21 months ago by Vincent J. Carey, Jr.6.2k

Latest awards to Vincent J. Carey, Jr.

Appreciated 17 months ago, created a post with more than 5 votes. For edX online course introducing Bioconductor now up and running
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For C: how can I install packages in docker/R/bioconductor so that they persist?
Centurion 4.3 years ago, created 100 posts.

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