User: joseph

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joseph40
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Posts by joseph

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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 1 day ago by joseph40 • updated 7 hours ago by Peter Langfelder1.3k
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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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by joseph40 • updated 7 weeks ago by Guangchuang Yu690
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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 12 weeks ago by joseph40 • updated 12 weeks ago by Lluís R270
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Can I apply WGCNA on unmatched time point microarray data and clinical data?
... When I use WGCNA, I usually have matched microarray data and clinical data, which means for each patient and each time point, the microarray data and clinical data are matched. However, some of the clinical data are coming out later, like the antibody, usually, Ab will be tested after 1 or 2 months, ...
wgcna written 3 months ago by joseph40
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How to solve out the misunstanding of fake "red" "green" on the heatmap
... I have lots of work need to use heatmap, however I find a problem that sometimes mislead to interpret the data if only by the heatmap visualization.  For example, I have several time points or groups data, the significant differential expression gene from each group should be different. As, Group ...
pheatmap written 3 months ago by joseph40 • updated 3 months ago by Gavin Kelly250
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Comment: C: clusterProfiler setup specified order
... Could you please clarify how to place the specific order on the x-axis? And keep some groups even they don't have enriched result, just to show the longitudinal data,   ...
written 3 months ago by joseph40
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Comment: C: clusterProfiler setup specified order
... I use entrezID for both of them, but has the error as > egmt_kegg <- enricher(DEG_Day9_ENTREZID, TERM2GENE = c_kegg, +                       pvalueCutoff = 0.1, pAdjustMethod = "BH", universe, +                       minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2) Error in as.vector(x, m ...
written 3 months ago by joseph40

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