User: adR

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adR50
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Posts by adR

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Comment: C: genes not mapping to ENTREZID
... Thanks, Joe for your answer! Actually, I did not design the study originally but they aim to answer both. Could please direct me on how to do BLASTing?. Where to access it! ...
written 7 days ago by adR50
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Comment: C: genes not mapping to ENTREZID
... Hi Kevin, Thanks for answering my question. Here are three genes that I did not find their KEGG IDs or their ENTREZID. ADCK3, AES, AF09010 ...
written 7 days ago by adR50
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genes not mapping to ENTREZID
... Hi Dear Scientists I want to ask a simple question but important to me. My question is, I have a list of DEG between the two conditions. While converting gene Symbole to their biological IDs(ENTREZID) few genes failed to map. Since they don't have ENTREZID, they aren't related to any KEGG pathway ...
gene pathway kegg entrezid written 7 days ago by adR50 • updated 7 days ago by waeemarjuriya0
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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 9 days ago by adR50
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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 6 weeks ago by adR50 • updated 6 weeks ago by ATpoint44k
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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 6 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 9 weeks 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 9 weeks 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 9 weeks ago by adR50 • updated 9 weeks ago by Kevin Blighe69k
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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 10 weeks ago by adR50

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