User: krc3004

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krc300410
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Posts by krc3004

<prev • 8 results • page 1 of 1 • next >
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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 6 weeks 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 6 weeks ago by krc300410 • updated 6 weeks ago by Michael Love14k
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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 3 months ago by krc300410 • updated 3 months ago by Mike Smith2.1k
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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 4 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 5 months ago by krc300410 • updated 4 months ago by b.nota290
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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 6 months ago by krc300410 • updated 6 months ago by Lluís R300
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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 6 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 6 months ago by krc300410 • updated 6 months ago by Martin Morgan ♦♦ 20k

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