User: psutton

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psutton0
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Posts by psutton

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Comment: C: ReportingTools publish(): no image when .modifyDF argument is included
... Thanks! I'll look into that. ...
written 7 days ago by psutton0
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Comment: C: ReportingTools publish(): no image when .modifyDF argument is included
... Thank for you this helpful information! The default argument of `.modifyDF` makes sense. However, in this particular case, it appears that `makeDESeqDF` works on `data.frames` created by `DESeq` (not `DESeq2`) after running `nbinomTest`. 1) The DESeq example from the vignette works perfectly: ...
written 7 days ago by psutton0
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ReportingTools publish(): no image when .modifyDF argument is included
... I am learning about using ReportingTools for DESeqDataSet. Using the example in the [user guide][1]: ``` library(DESeq2) library(ReportingTools) data(mockRnaSeqData) conditions <- c(rep("case",3), rep("control", 3)) mockRna.dse <- DESeqDataSetFromMatrix(countData = mockRnaSeqData, ...
reportingtools written 7 days ago by psutton0 • updated 7 days ago by James W. MacDonald49k
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Comment: C: go_bp table in custom OrgDb package
... I was able to modify `AnnotationForge` so that it would create `go_bp, go_cc, go_mf, go_bp_all, go_cc_all`, and `go_mf_all` tables for me. However, it is a bit hacky, because there were a number of issues with the exact spelling and case of field names in the SQLite tables, which I partly describe ...
written 11 days ago by psutton0
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topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
... `topGO::annFUN.org()` has the following lines: ``` ## function annFUN.org() to work with the "org.XX.eg" annotations annFUN.org <- function(whichOnto, feasibleGenes = NULL, mapping, ID = "entrez") { # [some lines have been omitted] geneID <- keyName[tolower(ID)] .sql <- past ...
topgo annotationforge written 14 days ago by psutton0
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Comment: C: go_bp table in custom OrgDb package
... Hi Federico, I tried `limmaquick2pca2go`, but it failed with an error message: ``` Error in goana.default(probesPC1pos_ENTREZ, bg_ENTREZ, species = organism) : Can't find gene ontology mappings in package org..eg.db ``` and looking at the `goana.default` code where it fails, it is looking for a ...
written 15 days ago by psutton0
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go_bp table in custom OrgDb package
... I am trying to use pcaExplorer's `pca2go()` function for functional enrichment analysis on genes with the highest principal component loadings. The function fails with the following error: ``` Ranking genes by the loadings ... Ranking genes by the loadings ... done! Extracting functional catego ...
annotation go annotationforge pcaexplorer written 16 days ago by psutton0 • updated 16 days ago by James W. MacDonald49k

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