Moderator: James W. MacDonald

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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: affycoretools package, HTA 2.0 annotation query
... If a function has a default, then by definition it isn't necessary to supply a value for that argument. But perhaps you are actually asking what value you should use? Again, the answer to your question can be found by reading the help page, this time for `rma`: ``` Description: Robust Multich ...
written 2 hours ago by James W. MacDonald49k
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Answer: A: affycoretools package, HTA 2.0 annotation query
... You need to become familiar with the help system, and to check there to ensure you are doing things correctly. From `?getMainProbes`, we have: ``` Usage: getMainProbes(input, level = "core") Arguments: input: Either a character string (e.g., "pd.hugene.1.0.st.v1") or a Fea ...
written 4 hours ago by James W. MacDonald49k
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Answer: A: How do I creat an expressionset if there is no GDS listed on the GEO database?
... Have you read the [vignette][1]? You can just as easily get data from the GSE entry, or if you want the raw data you can use `getGEOSuppFiles`. I have personally never used the pipeline you outline, opting instead for getting the GSE directly. [1]: http://bioconductor.org/packages/release/bioc/v ...
written 5 days ago by James W. MacDonald49k
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Answer: A: Installing DESeq2 on Google Cloud
... It's better if you give all of the R output rather than what you think might be useful. This error often comes up if you are missing the xml headers, so you probably have to install libxml2-devel. Often there is something like ``` checking for pkg-config... /usr/bin/pkg-config checking for xml2-c ...
written 6 days ago by James W. MacDonald49k
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Answer: A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
... You can get data for that organism from the `AnnotationHub`: ``` > library(AnnotationHub) > hub <- AnnotationHub() > query(hub, c("olea europaea", "orgdb")) AnnotationHub with 3 records # snapshotDate(): 2018-10-24 # $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ # $species: Olea ...
written 7 days ago by James W. MacDonald49k
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Comment: C: Unable to install packages
... They all failed with what message? ...
written 8 days ago by James W. MacDonald49k
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Comment: C: Unable to install packages
... Again, that doesn't help. Your original complaint was that you couldn't install recommended packages, with no mention about DESeq2. Now you say something cryptic about some packages working and others not working. Put yourself in our shoes. How could anybody read what you have said and use that to h ...
written 8 days ago by James W. MacDonald49k
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Answer: A: Unable to install packages
... This isn't a Bioconductor question! None of the packages you mention are part of Bioconductor. In future you should ask questions about basic R stuff on r-help@r-project.org That said, the packages you mention are all in the set of *recommended packages*, and if you installed R as a privileged user ...
written 8 days ago by James W. MacDonald49k
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Answer: A: DEP p.val adjustment
... Have you read the help page for `test_diff`? It says: ``` Value A SummarizedExperiment object containing FDR estimates of differential expression ``` And FDR is generally assumed to mean Benjamini and Hochberg's method (for example, if you ask `p.adjust` to use `fdr`, you get `BH`). ...
written 11 days ago by James W. MacDonald49k
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Comment: C: Problem concerning the Probe_Id / ProbeID and illuminaHumanv4PROBEQUALITY
... I don't use beadarray, personally, as any Illumina data I get can be read in using `read.ilmn` in limma. And a quick download of some Illumina Human HT12 v4 data from GEO indicates to me that there isn't a column called Probe_Id, so I'll have to take your word on that one. I also cannot find a funct ...
written 12 days ago by James W. MacDonald49k

Latest awards to James W. MacDonald

Scholar 3 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 3 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Good Answer 3 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 4 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Appreciated 4 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Good Answer 4 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 4 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 4 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 5 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 5 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Teacher 5 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 5 months ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Scholar 5 months ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Popular Question 5 months ago, created a question with more than 1,000 views. For Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Scholar 6 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Scholar 6 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 6 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 7 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Scholar 7 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?

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