User: joseph

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joseph40
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Posts by joseph

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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 4 weeks ago by joseph40 • updated 4 weeks ago by Lluís R210
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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 4 weeks 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 6 weeks ago by joseph40 • updated 6 weeks ago by Gavin Kelly180
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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 7 weeks 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 7 weeks ago by joseph40
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Comment: C: clusterProfiler setup specified order
... should I update to the latest version? I install the ver-3.4.1. The one you fixed in your developed version? BTW, after compareCluster(), might be some time point not have the gene clusters, but in order to present the time-course data, can I keep show up all time points data, even if some of them ...
written 7 weeks ago by joseph40
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Comment: C: clusterProfiler setup specified order
... list = list(Day1 = Day1, Day2 = Day2, Day3 = Day3......) levels(list) = c("Day1","Day2","Day3"....) lx = compareCluster(list) dotplot(lx) ...
written 7 weeks ago by joseph40
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Answer: A: clusterProfiler setup specified order
... And one more problem when I use enricher() function, also return no gene mapped: egmt_go <- enricher(DEG_Day9_ENTREZID, TERM2GENE = c_go, +                     pvalueCutoff = 0.5, pAdjustMethod = "BH", universe, +                     minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2) --> No ...
written 7 weeks ago by joseph40
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ID unmatched in pathview
... When I currently use pathview to present the KEGG pathway, the errors always are coming from multiplex pathways. It looks about unmatched gene ID. Here’s the codes and error warnings. > pathview(gene.data = datainv,pathway.id="04668",species="hsa",out.suffix = "TNF Signaling Pathway",kegg.native ...
pathview written 7 weeks ago by joseph40 • updated 4 weeks ago by Mataivic0
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clusterProfiler setup specified order
... I have time-course data as "Day1", "Day2"....., when I create the list for compareCluster(), I have named the order as levels(list) = c("Day1","Day2"....), and I check the compareCluster() result, CompGO@compareClusterResult$Cluster, shows the order is "Day1", "Day2".... However, when I plot the dat ...
clusterprofiler written 7 weeks ago by joseph40

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