User: arom2

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arom20
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Posts by arom2

<prev • 17 results • page 1 of 2 • next >
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Comment: C: WGCNA ranking of HUB genes
... Hi Lluis R., I actually still have a bit of confusion about this. I was hoping to get a list of the genes that have the highest module membership (HUB genes) within each module. From the code that you helped me with earlier, I found some genes were repeated in the lists from multiple modules. I fou ...
written 15 months ago by arom20
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Comment: C: WGCNA ranking of HUB genes
... Great, thank you!! I am not sure I completely understand the difference, but as long as this outputs representative HUB genes of the modules, then I am satisfied.   ...
written 15 months ago by arom20
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WGCNA ranking of HUB genes
... Hi, I am trying to analyze a set of particular genes that are all within a module in addition to the HUB genes of that module. I am finding that when I extract the list of genes with the highest module membership at varying lengths, the genes that populate that list slightly change in their ranking ...
wgcna hub written 15 months ago by arom20 • updated 15 months ago by Lluís R370
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Comment: C: WGCNA exporting for Visant visualization
... Great - thank you for spending the time to assist me with these commands! And yes, I accidentally posted the column headers used in the tutorial and not my particular labels. Now everything works perfectly! Maybe now you can help me figure out what all the data means.... :) ...
written 15 months ago by arom20
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Comment: C: WGCNA exporting for Visant visualization
... I'm still getting an error with my code when I select for those genes (listed in character 'IGFs'). I've validated that the genes names are present in the grey module, and I can create the Visant output for the entire module. However when I attempt the export after using the select function, I recei ...
written 15 months ago by arom20
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Comment: C: WGCNA exporting for Visant visualization
... Thank you, Peter. That makes sense but I am having a difficult time building the proper command that preserves the dimensions of the array with logical vectors. Are you sure about subsetting the adjMat argument or should I subset the list of names prior to that command. Code that I've tried: &g ...
written 15 months ago by arom20
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WGCNA exporting for Visant visualization
... Hi, I am trying to examine the connections of a particular list of genes between networks. When creating an edge file for Visant using the exportNetworkToVisANT function, is there a way to subselect a particular set of genes by their name rather than their rank in soft connectivity? They are not th ...
wgcna visant written 15 months ago by arom20 • updated 15 months ago by Peter Langfelder1.5k
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Change the FDR in DEXSeq
... To Whom It May Concern, Using DEXSeq, I am attempting to run an analysis of differentially used exons between two treatments groups at different False Discovery Rates (10%, 5%, and 1%). Yet the commands for running the test (testForDEU ) and retrieving results (DEXSeqResults) seem to have no argume ...
fdr padj written 21 months ago by arom20 • updated 21 months ago by Jakub30
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Comment: A: DESeq2 Model matrix design: Merging large RNAseq projects
... Hi Michael,  Thank you! This is a much better approach. -Amie ...
written 21 months ago by arom20
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DESeq2 Model matrix design: Merging large RNAseq projects
... To Whom It May Concern, I have been analyzing two large RNAseq projects separately and successfully. Recently, it was suggested that I merge the analyses so that normalized gene counts could be compared (not statistically) between the two experiments while also retaining the ability to perform stat ...
rnaseq deseq2 batch effect model.matrix written 21 months ago by arom20

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