User: joseph

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joseph40
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Posts by joseph

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Comment: C: RNseq data for WGCNA
... Here's the data link: https://bri.box.com/s/412z4zvjerypzffk51ptv368u6l5pxlf load("Filtered and annotated Count data.Rdata") RawCount_all_new, gene_annotation_new, Phenotype_all #------------------------------------------------------------------------------------------------# # Removing genes th ...
written 2.2 years ago by joseph40
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Comment: C: RNseq data for WGCNA
... Thanks. I'm not sure if few modules that I get looks "normal". Yes, I would like to have more modules. Meanwhile, the module-trait correlations are pretty low, I wonder to figure it out whether my data processing problem or it's the real of the data. ...
written 2.2 years ago by joseph40
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RNseq data for WGCNA
... I face some problem when I apply WGCNA in the RNseq data. Here’s the thing, I have the raw court data, which looks like as: head(RawCount_all_Filter)                 P6_A1 P6_A2 P6_A3 P6_A4 P6_A5 P6_A6 P6_A7 P6_A8 P6_A9 P6_A10 P6_A11 P6_A12 P6_B1 P6_B2 P6_B3 P6_B4 P6_B5 P6_B6 P6_B7 P6_B8 ENSG000 ...
wgcna written 2.2 years ago by joseph40 • updated 2.2 years ago by Peter Langfelder2.3k
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Meta-analysis with WGCNA
... I’m doing the meta-analysis on bunch of microarray data. There are from patients, with several time points before and after treatment. Actually, I’m interested in the post-treatment data (e.g. Day7), I wonder if reasonable only use normalized Day7 data to conduct the network construction, or in orde ...
wgcna written 2.3 years ago by joseph40 • updated 2.3 years ago by Lluís Revilla Sancho530
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WGCNA works on time course data
... Hi, I have a time-course microarray data. 7 subjects, each one has several time points (Day0, Day10, Day20, and Day30). And the trait data also have the same time point for every subject.  I wonder if make sense to pool all time points data together to construct the network and then correlate with ...
wgcna written 2.3 years ago by joseph40 • updated 2.3 years ago by Peter Langfelder2.3k
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Get bugs from pathview package
... Hi, I get some errors when I run the demo data: > data(gse16873.d) > data(demo.paths) > i <- 1 > pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = + demo.paths$sel.paths[i], species = "hsa", out.suffix = "gse16873", + kegg.native ...
pathview written 2.5 years ago by joseph40
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Comment: C: odd results "No enrichment found in any of gene cluster"
... In the compareCluster documents,  I can't find the default qvalueCutoff setting. In the above situation, no enrichment can be found when pvalueCutoff = 1, but 2 enrichment show up when set q = 1. I suppose the default q had been set less than 1. Is that right? ...
written 2.5 years ago by joseph40
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Comment: C: odd results "No enrichment found in any of gene cluster"
... I can understand the principle of gene enrichment. I just so surprised about nonpathway can be matched because the list is approx 1000+, even without significance (I set pvalueCutoff = 1), should have some gene match to KEGG pathway. I doubt if the list feature causes the problem? I check several ti ...
written 2.5 years ago by joseph40
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odd results "No enrichment found in any of gene cluster"
... I have two gene list as below, one of them is able to obtain an enriched KEGG pathway, the other one cannot. I consolidate them to one list, and carry on the KEGG enrichment, none of pathway has been found. The link of .Rdata of these lists, please use list, list_edge, list_limma to access. https ...
clusterprofiler written 2.5 years ago by joseph40 • updated 2.5 years ago by Guangchuang Yu1.1k
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The cor and corp values in verboseScatterplot don't match with cor, corPvalueStudent results
... The cor and cor p value in the verboseScatterplot don't match with cor() and corPvalueStudent() results. The codes as below:   geneTraitSignificance = as.data.frame(cor(VAX_Expr, sel_trait, use = "p"))   GSPvalue = as.data.frame(corPvalueStudent(as.matrix(geneTraitSignificance), nSamples))   verbo ...
wgcna written 2.6 years ago by joseph40 • updated 2.6 years ago by Lluís Revilla Sancho530

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For limma design and contrast matrix for paired samples

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