User: Christopher T Gregg

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c**********@neuro.utah.edu

Posts by Christopher T Gregg

<prev • 21 results • page 2 of 3 • next >
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biomaRt error
... Hi, I am reporting a biomaRt error noted during some work. The code did not return the flanking sequences of a SNP. > getBM(attributes=c('refsnp_id', 'chr_name', 'chrom_start', 'allele', 'c57bl_6j', 'cast_eij', 'upstream_flank','downstream_flank'), filters=c("snp_filter"), values=( "rs6171921" ...
snp biomart written 6.8 years ago by Christopher T Gregg210
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Comment: C: edgeR logFC
... Thank you, Gordon. I appreciate you helping to clarify this for me. best wishes, Chris On Jan 15, 2013, at 4:30 PM, Gordon K Smyth wrote: > Or else look at the help page for glmLRT, which says: > > "The data frame table contains the following columns: > logFC: log2-fold change of ex ...
written 6.8 years ago by Christopher T Gregg210
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edgeR logFC
... Hello, I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10. I was unable to see this information in the manuals. Thank you very much. best wishes, Chris [[alternative HTML version deleted]] ...
written 6.8 years ago by Christopher T Gregg210 • updated 6.8 years ago by Gordon Smyth39k
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design model EdgeR
... Hi, We are working on a glm analysis in EdgeR and voom() and I am hoping we can help with our design. Currently, we are getting errors. We have 18 RNA-Seq biological replicates (samples), each sample has two columns of counts for each tag, one for the maternal allele and one for the paternal alle ...
edger written 7.4 years ago by Christopher T Gregg210 • updated 7.4 years ago by Gordon Smyth39k
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DESeq error with glm.fit during estimateDispersions
... Hi, I am working on a multifactor analysis using DESeq. When I call estimateDispersions I get the following error: cdsFull <- estimateDispersions( cdsFull, method="pooled-CR", modelFormula = count ~ sample+allele+allele:diet) Error in glm.fit(mm, y, family = MASS::negative.binomial(initialGues ...
deseq written 7.5 years ago by Christopher T Gregg210 • updated 7.5 years ago by Simon Anders3.6k
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DESeq problems with plotDispEst using pooled-CR
... Hi, I have been using the pooled-CR method of estimating dispersions with DESeq. I wish to plot the fit using the approach presented in the vignette. When I use this function with plotDispEsts(cps, "pooled") it appears to work, however when I use plotDispEsts(cds, "pooled-CR") it fails. I would ...
written 7.6 years ago by Christopher T Gregg210 • updated 7.6 years ago by Wolfgang Huber13k
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Updating Package Versions from SVN
... Hi, I am attempting to update DESeq with the latest version in found in Subversion. I have downloaded the latest version of DESeq to my hard drive using: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq What steps do I take to incorporate the features of the new version in ...
deseq written 7.6 years ago by Christopher T Gregg210 • updated 7.6 years ago by James W. MacDonald51k
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Comment: C: how to get a list of the genes in each module in WGCNA
... Thank you, Marco. We will work through this material and see how it goes. best wishes, Chris On Jan 19, 2012, at 1:12 AM, Manca Marco (PATH) wrote: Dear Chris you might take advantage of the rich set of tutorials that Langfelder and Horvath have made available on their WGCNA page ( http://ww ...
written 7.8 years ago by Christopher T Gregg210
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Answer: A: goseq problem
... The confusion for me seems to be from different variables in different explanations of the pipeline. My interpretation is the DEgene vector defined in the manual is the same as the gene.vector in the R script: gene.vector<-as.integer(assayed.genes %in% de.genes) Thus, one estimates the PWF wit ...
written 8.0 years ago by Christopher T Gregg210
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goseq problem
... Hi, I am having the same problem, but don't understand Naomi's solution. What is the DEgene vector supposed to be if not my de.gene list? Thank you for your help. best wishes, Chris Christopher Gregg, PhD. Assistant Professor, Neurobiology and Anatomy Adjunct Professor, Human Genetics 323 Wintr ...
written 8.0 years ago by Christopher T Gregg210

Latest awards to Christopher T Gregg

Great Question 5.5 years ago, created a question with more than 5,000 views. For edgeR logFC
Popular Question 5.5 years ago, created a question with more than 1,000 views. For GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Popular Question 5.5 years ago, created a question with more than 1,000 views. For edgeR logFC
Popular Question 5.5 years ago, created a question with more than 1,000 views. For GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Popular Question 5.5 years ago, created a question with more than 1,000 views. For edgeR logFC

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