Moderator: James W. MacDonald

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Joined:
15 years, 5 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 • 5,051 results • page 2 of 506 • next >
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Answer: A: Problem using biocLite() to update packages
... One of the issues with Windows is that you lock any dir that is being accessed, like in any way, by any process. As an example: > .libPaths() [1] "C:/Users/jmacdon/AppData/Roaming/R/win-library/3.4" [2] "c:/Program Files/R/R-3.4.1/library" Now I open a command prompt and do this: C:\Users\jm ...
written 13 days ago by James W. MacDonald45k
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Answer: A: How to prevent readDNAStringSet() function from switching masked sequences (lowe
... The simple answer is 'Because that is how it is designed to work'. From ?DNAString, which you should always check first: Details: The DNAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also ...
written 13 days ago by James W. MacDonald45k
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Comment: C: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
... Have you looked at the help page for .libPaths? It's pretty comprehensive. ...
written 13 days ago by James W. MacDonald45k
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Answer: A: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
... This usually comes up when you are trying to use a network directory for your library path. That's not (IMO) usually worth the effort, so the quick fix is to set your .libPaths to somewhere on your computer's hard drive. An alternative might be to map the directory share to a drive path, like Z:, bu ...
written 13 days ago by James W. MacDonald45k
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Answer: A: Strong upwards correlation between log fold change and average log expression in
... From ?plotMD, specifically the Details section If 'object' is an 'MArrayLM' object, then the plot is an fitted model MD-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis. Since you have fit a cell means model (e.g., your coefficients ...
written 14 days ago by James W. MacDonald45k
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Comment: C: GO-terms delivered by GOstats hyperGTest() do not exist in my universe
... You will have to provide a self-contained example to show the problem for anybody to help.   ...
written 14 days ago by James W. MacDonald45k
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Answer: A: How is microarray normalization done in PIANO?
... In the vignette it says this on page 6: The loadMAdata function will normalize the raw data (by default using the plier algorithm) ...
written 17 days ago by James W. MacDonald45k
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Answer: A: gcrma error " 'Calloc' could not allocate memory"
... You could try justGCRMA, which is supposed to be a bit less memory intensive. But 224 arrays is a lot if you don't have a reasonable amount of RAM. The obvious other alternatives are to get more RAM, or to use a large-ish EC2 instance and the Bioconductor AMI.   ...
written 17 days ago by James W. MacDonald45k
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Answer: A: mas5 normalisation giving negetive value after using exprs()
... There is no guarantee that you won't have negative values from the MAS5.0 algorithm. It's simply a robust average of the PM - MM probe intensities, scaled to (in the case of the defaults) a value of 500. That's usually a large enough value to scale to, in order to eliminate negative values, but ther ...
written 17 days ago by James W. MacDonald45k
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Comment: C: Best DEG tool for datasets with FPKM counts?
... Please remember to use ADD COMMENT to add comments. The gene symbols you show like 1700003F12Rik (and yes, they are gene symbols) are RIKEN genes. Or rather, RIKEN ESTs that the RIKEN project generated way back in the dark old days of like 2000 or so. These days those are (probably) mostly speculat ...
written 21 days ago by James W. MacDonald45k

Latest awards to James W. MacDonald

Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Commentator 5 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 6 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 6 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 6 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 8 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 9 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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