User: krc3004

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krc300410
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1 year, 7 months ago
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k******@med.cornell.edu

Posts by krc3004

<prev • 9 results • page 1 of 1 • next >
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PANTHER.db- external pointer error
... Hi, I'm trying to use PANTHER.db to conduct pathway analysis on a set of differentially expressed genes, and I'm running into an error when loading PANTHER.  I install as usual: biocLite("PANTHER.db") library(PANTHER.db) But when I type PANTHER.db at the console, I obtain the following error: ...
goseq gene ontology pathway analysis pantherdb written 12 months ago by krc300410 • updated 12 months ago by James W. MacDonald48k
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Comment: C: DESeq: large difference in number of replicates per condition
... Michael, thanks very much for your help!  I will proceed without downsampling. ...
written 14 months ago by krc300410
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DESeq: large difference in number of replicates per condition
... Hi all, I have a general question about the model estimation used by DESeq.  There have been many posts on whether or not DESeq works well with a small number/no replicates, but I'm wondering if it's appropriate to use DESeq for differential analysis across two conditions, where one condition has a ...
rnaseq deseq2 differential expression written 14 months ago by krc300410 • updated 14 months ago by Michael Love20k
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PANTHER.db function not found
... Hi all, I'm using PANTHER.db to run some enrichment analysis and am trying to use the function pthOrganisms to restrict the database to mouse.  More specifically, the code is: pthOrganisms(PANTHER.db) = "MOUSE" However, I obtained the following error: Error: could not find function "pthOrganisms ...
biomart goseq pantherdb written 16 months ago by krc300410 • updated 16 months ago by Mike Smith3.1k
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Comment: C: Getting Differentially Expressed Genes from GOSeq Categories
... Hi Lluis, thanks for your reply.  In diff_exp_ensembl, a gene is differentially expressed according to DESeq- i.e. any gene with adjusted p-value less than some cutoff.   ...
written 17 months ago by krc300410
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Getting Differentially Expressed Genes from GOSeq Categories
...   Hi all, There have been a number of questions asked on this topic (I've linked the relevant threads below), but I'm not sure if anyone has found a working solution.  I have run GOSeq on my gene set and am looking to identify the genes in each category (numDEInCat).  Here is what I've done so far ...
annotate biomart category goseq gene ontology written 17 months ago by krc300410 • updated 17 months ago by b.nota300
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topGO gene names/ensembl IDs
... Hi All, I have performed a differential expression analysis using DESeq2, and would now like to analyze enriched GO terms using the topGO package.  However, I am having difficulty formatting the gene names for input.  Here's what I have so far. ## create named vector of p values GO_genes = setNam ...
biomart topgo deseq2 gene ontology written 19 months ago by krc300410 • updated 19 months ago by Lluís Revilla Sancho430
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Answer: C: rowRanges in Summarized Experiment changes counts
... Never mind!  Silly mistake on my part- the names in exons.genes weren't in the same order as the row names in rna_raw_counts_no_tech_rep_ordered, so things got jumbled, not changed.  Fixed the order and everything looks good.  ...
written 19 months ago by krc300410
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rowRanges in Summarized Experiment changes counts
... Hi all, First post here, so apologies if I haven't explained anything clearly/followed standard guidelines. I'd like to create a summarized experiment object for downstream analysis of my count data from RNA seq analysis.  The way I do this is something like this: rna_raw_counts_no_tech_rep_orde ...
rnaseq deseq2 summarizedexperiment rangedsummarizedexperiment written 19 months ago by krc300410 • updated 19 months ago by Martin Morgan ♦♦ 22k

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