Moderator: James W. MacDonald

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15 years, 10 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

<prev • 5,206 results • page 1 of 521 • next >
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Answer: A: Uniprot.ws getting Function [CC]
... OK, fixed now. This is in the devel version of Bioconductor, as the release version is frozen. The updates will propagate through the build system in the next couple of days. > select(ws, "P23434", "FUNCTION","UNIPROTKB") Getting extra data for P23434 'select()' returned 1:1 mapping between key ...
written 1 day ago by James W. MacDonald46k
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Comment: C: Uniprot.ws getting Function [CC]
... I'll take a look at adding that. Right now you can return the comments column, but it just tells you what type of comments there are, without returning the individual columns themselves: > ws <- UniProt.ws() select(ws, "P23434", c("COMMENTS"), "UNIPROTKB") > Getting extra data for P23434 ...
written 1 day ago by James W. MacDonald46k
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Comment: C: Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
... I tried on Windows and Linux and get the same result as the OP: > library(BiocInstaller) Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help > biocLite("rnaseqGene") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30). Ins ...
written 2 days ago by James W. MacDonald46k
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Answer: A: Uniprot.ws getting Function [CC]
... The UniProt.ws package only provides a subset of the data you can get directly from the UniProt website. You can see what's available by loading the package and then calling the columns function: > ws <- UniProt.ws() > columns(ws) [1] "3D" "AARHUS/GHENT-2DPAGE" ...
written 2 days ago by James W. MacDonald46k
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Answer: A: makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
... Unless you are answering your own question, please don't use the 'Add your answer' box. the ADD COMMENT link is what you should use to add comments. The issue here is that the UCSC Genome Browser is a bit of a moving target, and they do tend to make changes that end up breaking our tools. In this c ...
written 6 days ago by James W. MacDonald46k
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Answer: A: Error and warning message when reading the ballgown object
... I think you already got the advice you need: Error in ballgown(dataDir = "/fast/123456/Analysis02/DGE/prr01", : intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample. Did you check the i_data.ctab file for each sample? ...
written 11 days ago by James W. MacDonald46k
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Comment: C: Processing agilent data by limma
... Code snippets are not useful! Unless you show exactly what you did, you are expecting people to guess at what you might have done, and most people are too busy to bother with such things. You need to show a short, self-contained (e.g., anybody can run) bit of code to show exactly what you did and wh ...
written 11 days ago by James W. MacDonald46k
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Answer: A: affymetrix miRNA microarray analysis, (package mirna30cdf)
... You cannot use the affy package for analysis of this array, because it re-uses the same probes for multiple probesets. The only way to analyze this array is to use oligo. Is there some reason you don't want to do so? ...
written 12 days ago by James W. MacDonald46k
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Answer: A: How does edgeR cpm function calculate log(CPM) values?
... The cpm function computes log2 counts/million, as stated in the help page for the function. But remember that you are computing counts/million counts. If you start with 0 counts, bump that up to 1 with a prior count of 1, and then divide by the total counts for that sample (in millions), unless you ...
written 13 days ago by James W. MacDonald46k
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Answer: A: Log2 vs Quantile normalization
... Taking logs and doing a quantile normalization are completely different things, so there is no sense in comparing them. In addition, this support site is intended for helping people who are having problems understanding Bioconductor tools, rather than general questions about data transformations. A ...
written 13 days ago by James W. MacDonald46k

Latest awards to James W. MacDonald

Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 11 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 11 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 12 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 12 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 12 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 13 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 13 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 13 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 13 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 14 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 14 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

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