Moderator: James W. MacDonald

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17 years, 2 months ago
Email:
j******@u.washington.edu

I am a core member of the Bioconductor project, and I work for the University of Washington in the Department of Environmental and Occupational Health Sciences. I telecommute from Ann Arbor, MI (Go Blue!) because how will I be able to suffer the enduring pain of being a UM football fan if I can't go to the games?

Posts by James W. MacDonald

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Comment: C: tx2gene for xenopus LAEVIS
... Please try to format your posts reasonably. I had to go through and fix the blob of text you wrote in order to be able to see what you are asking. There are ways of importing the FASTA names into R, but probably the easiest is to use the Biostrings package: ``` fastas <- readDNAStringSet() ``` ...
written 13 hours ago by James W. MacDonald50k
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Answer: A: BiocCheck gives 'Error in readLines(file, skipNul = TRUE) : cannot open the conn
... Package development questions should be directed to bioc-devel@r-project.org ...
written 19 hours ago by James W. MacDonald50k
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Answer: A: Is mm10.p6 available as BSgenome?
... You could just [make your own version][1]. [1]: http://bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf ...
written 19 hours ago by James W. MacDonald50k
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Answer: A: tx2gene for xenopus LAEVIS
... Non-model organisms can be tough. You do apparently have GenBank IDs, so hypothetically you could map to Gene ID using an OrgDb package. ``` > library(AnnotationHub) > hub <- AnnotationHub() |======================================================================| 100% snapshotDate(): 20 ...
written 19 hours ago by James W. MacDonald50k
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Answer: A: samples.txt?how to generate
... You don't really need a file called samples.txt. You just need a `data.frame` that contains columns that describe pertinent information about your samples, where the `row.names` of the `data.frame` are the same as your samples. You could recreate the `data.frame` used in the DESeq2 vignette like thi ...
written 1 day ago by James W. MacDonald50k
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Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... Yes. See my first answer. As an example, cribbed from `?DGEList` ``` > y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4) > library(org.Hs.eg.db) ## pretend like these are human genes > row.names(y) <- keys(org.Hs.eg.db)[1:nrow(y)] > annot <- select(org.Hs.eg.db, row.names(y), c( ...
written 25 days ago by James W. MacDonald50k
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Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... And never mind all that. You won't be able to use `goana`; as the help page says, you can look at `?alias2Symbol` to get all the organisms that you can use: ``` 'species' can be any character string XX for which an organism package org.XX.eg.db exists and is installed. The only requirement ...
written 26 days ago by James W. MacDonald50k
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Comment: C: goana and "No annotated genes found in universe" even with Entrez gene ids
... I should note that there appears to be a 1-1 correspondence between SGD and Gene IDs: ``` > z <- select(org.Sc.sgd.db, keys(org.Sc.sgd.db), "ENTREZID") 'select()' returned 1:1 mapping between keys and columns ``` But if you didn't get the message that there is a 1:1 mapping, you would need to ...
written 26 days ago by James W. MacDonald50k
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Answer: A: goana and "No annotated genes found in universe" even with Entrez gene ids
... Your `DGELRT` object dgelist_qltest is a list, with a `genes` item that you can put things in. In general when you make the `DGEList` to begin with, you would put all the annotation in at that point. You could do something like ``` ## here I am assuming that your counts were in an object called 'co ...
written 26 days ago by James W. MacDonald50k
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Answer: A: Disagreement between results of two 'getBM' queries
... When you put lots of attributes in, you are doing some sort of join between different database tables, and it looks like the GO table might be messing you up. ``` > z <- head(ensembl2entrez_bio[!ensembl2entrez_bio$entrezgene_id %in% ensembl2entrez$entrezgene_id,1]) > z [1] "YBR225W" "YBR ...
written 29 days ago by James W. MacDonald50k

Latest awards to James W. MacDonald

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Appreciated 26 days ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 26 days ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Scholar 29 days ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Scholar 7 months ago, created an answer that has been accepted. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Popular Question 7 months ago, created a question with more than 1,000 views. For Saving/loading TxDb objects
Appreciated 7 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 7 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 7 months ago, created an answer that has been accepted. For A: Limma import .gpr file error
Scholar 7 months ago, created an answer that has been accepted. For A: Iterate through sever annotation database packages
Scholar 7 months ago, created an answer that has been accepted. For A: Probe to gene id conversion
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 7 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Different annotation obtained from hgu133a2.db and affymetrix annotation release
Scholar 7 months ago, created an answer that has been accepted. For A: Problems with "exonsBy" function from GenomicFeatures package
Scholar 7 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable

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