User: akridgerunner

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United States
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3 years, 4 months ago
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4 years, 5 months ago
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Posts by akridgerunner

<prev • 25 results • page 1 of 3 • next >
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Question about neqc and GEO illumina files
... Hello, I'm trying run raw data from GEO, GSE49454: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49454 GSE49454_RAW.tar contains: GPL10558_HumanHT-12_V4_0_R1_15002873_B.txt GPL10558_HumanHT-12_V4_0_R2_15002873_B.txt Both of these are probe description files without any signal data. R1 list ...
limma illumina geo neqc written 3.4 years ago by akridgerunner20 • updated 3.4 years ago by Gordon Smyth39k
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Comment: C: WGCNA automatic vs manual network creation
... Great, thanks! I read this some time ago and use signed network analysis. It looks like I confused the TOMtype setting with the networkType setting, and by omitting the latter was generating unsigned networks. My new effort now looks beautiful, with the two blocks from the automatic approach resembl ...
written 4.0 years ago by akridgerunner20
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Comment: C: WGCNA automatic vs manual network creation
... Thanks Peter I'm currently running: net = blockwiseModules(datExpr, power = 10, corType="bicor", deepSplit = 3, networkType = "signed", TOMType = "signed", minModuleSize = 100, numericLabels = TRUE, pamStage = TRUE, pamRespectsDe ...
written 4.0 years ago by akridgerunner20
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WGCNA automatic vs manual network creation
... Hello, I've created trees using what I thought were two relatively equivalent approaches, but I'm getting two very different results. Dr. Langfelder, if you're out there could you glance at this? For the first network I'm manually generating a tree from a single block of some ~17,000 probes. For t ...
wgcna written 4.0 years ago by akridgerunner20 • updated 4.0 years ago by Peter Langfelder2.2k
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Comment: C: limma design matrix question
... Thanks Aaron, done. ...
written 4.0 years ago by akridgerunner20
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limma design matrix question
... Hello, We're analyzing a two color microarray experiment with universal human reference RNA in the Cy3 green channel. Cy5 red is hybridized to either a monozygotic diseased twin (SLE_Affected), healthy twin (SLE_Healthy), or a healthy unrelated person (Control). Note I first created an MA list call ...
limma design and contrast matrix limma design matrix written 4.0 years ago by akridgerunner20 • updated 4.0 years ago by Aaron Lun25k
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WGNCA kME vs. kIM
... Hello, I've reviewed https://support.bioconductor.org/p/69858/#70116. I'm calculating module membership (MM) using geneModuleMembership = as.data.frame(cor(datExpr, MEs, use = "p")) Because kME is a more sophisticated approach as it includes error checking and other features, I also used signedKME( ...
wgcna written 4.1 years ago by akridgerunner20 • updated 4.1 years ago by Peter Langfelder2.2k
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WGNCA kME vs. kIM
... Hello, I've reviewed https://support.bioconductor.org/p/69858/#70116. I'm calculating module membership (MM) using geneModuleMembership = as.data.frame(cor(datExpr, MEs, use = "p")) Because kME is a more sophisticated approach as it includes error checking and other features, I also used signedKME( ...
wgcna written 4.1 years ago by akridgerunner20 • updated 3.1 years ago by Lluís Revilla Sancho510
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Comment: C: WGCNA network creation error
... As an update I filtered out a number of probes based on an arbitrarily selected mean low intensity threshold. This removed the "offending probes" and allowed for successful network creation. I'm still curious what Dr. Langfelder might have to say about this, or if we should modify the plugin to hand ...
written 4.2 years ago by akridgerunner20
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WGCNA network creation error
... Hello, I'm using the following to attempt network creation # Load the WGCNA package library(WGCNA) options(stringsAsFactors = FALSE); enableWGCNAThreads() load("1-data_input.Rdata") net = blockwiseModules(datExpr, power = 6, networkType = "signed", checkMissingData = TRUE, corType="bicor", ...
wgcna written 4.2 years ago by akridgerunner20 • updated 4.2 years ago by Peter Langfelder2.2k

Latest awards to akridgerunner

Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA cytoscape export question
Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA network creation error
Popular Question 3.4 years ago, created a question with more than 1,000 views. For LIMMA producing too many significant results
Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA corrupt TOM fails to export to Cytoscape
Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA Cohort Question
Popular Question 3.4 years ago, created a question with more than 1,000 views. For WGCNA automatic vs manual network creation
Popular Question 3.9 years ago, created a question with more than 1,000 views. For WGCNA automatic vs manual network creation

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