User: adR

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adR50
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Posts by adR

<prev • 57 results • page 2 of 6 • next >
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how to plot selected enriched pathways using emapplot
... Hi Biostars, I have a list of pathways but all of them are not related to my conditions of interest. So I would like to filter those only related to my questions and like to plot them using emaplot() function(a Bioconductor package called clusterProfiler) to see if they have interaction. Any sugg ...
R guangchuang yu clusterprofiler written 6 weeks ago by adR50 • updated 23 days ago by Biostar ♦♦ 20
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Two-dimensional hierarchically clustered heatmap
... Dear Scientist, I respectfully would like to get your feedback(tutorial) on the following questions. I have gene expression data from the same Biological replicates of two tissues of the brain(cortex and cerebellum) I want to know if Cortex and Cerebellum genes have similarities in their expression/ ...
cluster corrlation heatmap R written 11 weeks ago by adR50 • updated 11 weeks ago by ATpoint46k
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Comment: A: Complex Heatmap: Changing order of clusters
... @Kevin Blighe, I would like to add my questions here if possible? 1. How I could show those four clusters in a colors-a color bar for each cluster as indicated for the sample clustering on the top of this post. 2. Then, is it possible to extract the cluster genes(for example cluster 1 in the above ...
written 11 weeks ago by adR50
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Comment: C: gene network analysis for 3 conduation
... Hi Jeah, I have applied what you suggest in the link above. Here is the code in case you want to see it. I have 3 cross-correlation matrix crated as follow. la <- cor(t(li.A ), t(pa.A)) write.csv(la, "lc.csv") lb <- cor(t(li.B, t(pa.B)) write.csv(lb, "lb.csv") lc <- co ...
written 3 months ago by adR50
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Comment: C: gene network analysis for 3 conduation
... @Jean-Karim Heriche, Thank you so much for your quick answer. I will see the link you showed above. However, to make it clear, both tissues are from the same subjects of different conditions. So what I am studying is, how it looks like the interaction between liver and pancreas under those 3 differe ...
written 3 months ago by adR50
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gene network analysis for 3 conduation
... I would like to compare the gene network that exists in 3 different conditions (A, B, and C). For each condition, I have RNAseq data of two tissues (liver and pancreas). Therefore, I want to do a gene correlation network for these two issues of conditions A, B, and C. Eventually I would like to comp ...
gene network written 3 months ago by adR50 • updated 3 months ago by Kevin Blighe71k
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Comment: C: correlation matrix and working on signficant genes
... @Alex, Thank you again for your answers! However, **rcorr(t(m1),t(m2)) and rcorr(t(rbind(m1,m2))))** would give you the same result. Value differences you noticed in the heatmap_indices object is TRUE. This is because the heatmap_indices object does not represent the full correlation matrix rather ...
written 3 months ago by adR50
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Comment: C: correlation matrix and working on signficant genes
... Thank you so much Kevin! However, I may ask some tutorial on this correlation? Incase my question wasn't clear I might re-post it again or modifying it. ...
written 3 months ago by adR50
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Comment: A: correlation matrix and working on signficant genes
... @Alex, Thanks again for your feedback! I don't have informatics and R knowledge. I am just learning by doing using my data. I chose power 12 by mistake; the default in WGCNA is 6. The heatmap_indices object**(heatmap_indices <- test$r[1:n,(n+1):(2*n)])** represents the top-right block of the simi ...
written 3 months ago by adR50
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Comment: A: correlation matrix and working on signficant genes
... @Alex, Thank you so much! I will plot the full matrix then using gplots::heatmap2(). However, do you recommend converting the similarity matrix which I am interested in **(test$r[1:n,(n+1):(2*n)])** to be converted to the adjacency matrix before plotting as heatmap or in the graph? If so ...actuall ...
written 3 months ago by adR50

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