User: psutton

gravatar for psutton
psutton0
Reputation:
0
Status:
New User
Last seen:
5 months, 1 week ago
Joined:
7 months, 3 weeks ago
Email:
u*************@yahoo.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by psutton

<prev • 10 results • page 1 of 1 • next >
0
votes
4
answers
1.7k
views
4
answers
Comment: C: Urgent: Do GAGE applicable for non model species?
... I have a follow-up question about this approach. I ran KAAS on my non-model organism, and I understand your suggestion above changing the gene IDs (i.e. the row names of an expression data matrix) to the KEGG Orthology (KO) numbers assigned by KAAS before running gage. Since the multiple genes mig ...
written 5 months ago by psutton0
0
votes
1
answer
104
views
1
answers
Comment: C: DESeq2 lfcThreshold question: different numbers when filtering in results() vs.
... Thanks Michael, I think this section from the DESeq2 paper answers my question: "A common procedure is to disregard genes whose estimated LFC β_ir is below some threshold, | β_ir | ≤ θ. However, this approach loses the benefit of an easily interpretable FDR, as the reported P value and adjusted P v ...
written 6 months ago by psutton0
0
votes
1
answer
104
views
1
answer
DESeq2 lfcThreshold question: different numbers when filtering in results() vs. filtering afterwards?
... I have a question about lfcThreshold in DESeq2. In the sample code below, I use the airway demo data, have a variable lfcThreshold = log2(1.5). The variable `res1` contains results() without an lfcThreshold (i.e. default 0). Then, `res2` is the result of filtering res1 for abs(res1$log2FoldChange) ...
deseq2 written 6 months ago by psutton0 • updated 6 months ago by Michael Love25k
0
votes
1
answer
152
views
1
answers
Comment: C: ReportingTools publish(): no image when .modifyDF argument is included
... Thanks! I'll look into that. ...
written 7 months ago by psutton0
0
votes
1
answer
152
views
1
answers
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 months ago by psutton0
1
vote
1
answer
152
views
1
answer
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 months ago by psutton0 • updated 7 months ago by James W. MacDonald51k
0
votes
1
answer
219
views
1
answers
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 7 months ago by psutton0
0
votes
0
answers
136
views
0
answers
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 7 months ago by psutton0
0
votes
1
answer
219
views
1
answers
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 7 months ago by psutton0
0
votes
1
answer
219
views
1
answer
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 7 months ago by psutton0 • updated 7 months ago by James W. MacDonald51k

Latest awards to psutton

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 348 users visited in the last hour