User: Christopher T Gregg

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

Posts by Christopher T Gregg

<prev • 21 results • page 1 of 3 • next >
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Comment: C: edgeR calcNormFactors for paired counts
... Thank you, Ryan. We are comparing edgeR to some of these other options. I appreciate your point. best wishes, Chris On May 24, 2014, at 5:06 PM, Ryan > wrote: Hi Chris, I wouldn't go so far as to call myself an export on the subject of normalization, but that is what makes the most sense t ...
written 5.4 years ago by Christopher T Gregg210
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Comment: C: edgeR calcNormFactors for paired counts
... Terrific, Ryan. This was our thought as well and we are very grateful to have your expert advice. Thank you, Chris On May 24, 2014, at 4:41 PM, Ryan > wrote: Hi Chris, I think what you want to do here is normalize at the level of individuals. To that end, I would generate the full count mat ...
written 5.4 years ago by Christopher T Gregg210
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edgeR calcNormFactors for paired counts
... Hi, We are examining the use of edgeR to analyze allele-specific count data from RNASeq experiments. In these studies, each biological replicate (n=18) has two columns: one with counts from the maternal allele and the other with counts from the paternal allele for each gene. Thus, the data is pai ...
rnaseq normalization edger written 5.4 years ago by Christopher T Gregg210 • updated 5.4 years ago by Ryan C. Thompson7.4k
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Comment: C: RCytoscape: object 'graph' not found error
... Hi Paul, I will try this out. Thank you very much for your help and rapid reply. best wishes, Chris On Dec 31, 2013, at 2:34 PM, Paul Shannon > wrote: Hi Chris, Switching to a graphNEL -- which RCytoscape requires -- here below is some working graph-creation code. In addition to the vigne ...
written 5.8 years ago by Christopher T Gregg210
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Comment: C: RCytoscape: object 'graph' not found error
... Hi Paul, Thank you. This did resolve the problem. However, it revealed another issue that is also unclear. Would you mind commenting on the source of this error? Thank you for your help. best wishes, Chris > from [1] "ENSMUSG00000000037" "ENSMUSG00000000037" "ENSMUSG00000000037" "ENSMUSG00 ...
written 5.8 years ago by Christopher T Gregg210
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RCytoscape: object 'graph' not found error
... Hi, I have encountered an error with RCytoscape that is unclear to me. I have attached our script and data file and sessionInfo (at the bottom of the script) below. Our data is an adjacency matrix and we wish to construct a weighted network graph in Cytoscape. I am able to generate the graph obj ...
graph rcytoscape written 5.8 years ago by Christopher T Gregg210 • updated 5.8 years ago by Paul Shannon370
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looking for tools to study additive expression effects in gene pathways/networks
... Hi, We are seeking recommendations for approaches to study how gene expression effects may become additive within pathways. We have logFC values for genes differentially expressed in a comparison of control to treatment. We are interested in the following problem: Genes A and B exhibit a modest ...
pathways rgraphviz kegggraph written 6.4 years ago by Christopher T Gregg210
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GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
... Hi, I am encountering an error when attempting to retrieve data from the X chromosome using GViz. The error is unclear to me and I would greatly appreciate some help. The code and error and sessionInfo() are below. Please note that I have tried the code with and without ucscChromosomeNames=FALSE ...
biomart gviz written 6.5 years ago by Christopher T Gregg210 • updated 6.5 years ago by Robert Ivanek640
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Comment: C: biomaRt access for NCBIM37 build of mouse genome
... Thank you, Hans-Rudolf. I greatly appreciate this tip. best wishes, Chris On Mar 13, 2013, at 2:40 AM, Hans-Rudolf Hotz wrote: > Hi Chris > > use one of the archives. 'ensembl67' ("may2012.archive.ensembl.org") was the last ensembl release containing NCBIM37 (if I remember correctly). ...
written 6.6 years ago by Christopher T Gregg210
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biomaRt access for NCBIM37 build of mouse genome
... Hello, I am using biomaRt. I want to retrieve transcript start and stop info based on the NCBIM37 (mm9) build using getBM. I can't find this annotation in listMarts(archive =T). Is anyone aware of a simple solution? Thank you. best wishes, Chris > sessionInfo() R version 2.15.2 (2012-10- ...
biomart written 6.6 years ago by Christopher T Gregg210 • updated 6.6 years ago by Hotz, Hans-Rudolf400

Latest awards to Christopher T Gregg

Great Question 5.4 years ago, created a question with more than 5,000 views. For edgeR logFC
Popular Question 5.4 years ago, created a question with more than 1,000 views. For GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Popular Question 5.4 years ago, created a question with more than 1,000 views. For edgeR logFC
Popular Question 5.4 years ago, created a question with more than 1,000 views. For GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
Popular Question 5.4 years ago, created a question with more than 1,000 views. For edgeR logFC

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