User: nsmaan

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nsmaan10
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Posts by nsmaan

<prev • 15 results • page 1 of 2 • next >
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Comment: C: clusterprofiler: Pathview and dotplot
... My input looks like this: ---------------- data<-read.delim("test.txt") # File is tab-delimited #file contains columns of ENSEMBL, entrez, GENENAME, logFC, padj genes<-data$entrez[abs(data$logFC)>1.5 & data$padj<0.01 ] ego<- enrichGO(genes,OrgDb= org.Rn.eg.db,ont= ...
written 6 months ago by nsmaan10 • updated 6 months ago by Benn7.5k
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clusterprofiler: Pathview and dotplot
... Hello Experts. I have processed my RNA-seq data in a well-formatted text file (atleast i thought so..) that looks like this (~100+ genes) where i have Ensembl, entrezgene, gene(ID), group (up/down regulated), keggID, logFC, and padj, etc > head(ids) Ensembl entrezgene gene group kegg log ...
rna-seq written 6 months ago by nsmaan10 • updated 6 months ago by Benn7.5k
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Comment: C: pathway analysis: ReactomePA and clusterProfiler
... Thanks Ben!. This worked. ...
written 6 months ago by nsmaan10
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Comment: A: pathway analysis: ReactomePA and clusterProfiler
... My bad. Yes, i tried that too (in uppercase). When i try to read SYMBOL from my text file (shown in first post) eg = bitr(x, fromType="SYMBOL", toType="GENENAME", OrgDb="org.Rn.eg.db") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'S ...
written 6 months ago by nsmaan10 • updated 6 months ago by genomax70k
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Comment: A: pathway analysis: ReactomePA and clusterProfiler
... Thanks Ram. I tried orgDb="org.RN.eg.db" orgDb="org.Rn.eg.db" OrgDb="org.RN.eg.db" orgDb="org.Rn.eg.db" But none of them working. I also reinstalled BiocManager::install("org.Rn.eg.db", version = "3.8") Any more suggestions that I can try please? ...
written 6 months ago by nsmaan10 • updated 6 months ago by genomax70k
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pathway analysis: ReactomePA and clusterProfiler
... Hello to Forum experts once again: I am trying the step-by-step document examples provided for reactomePA and clusterprofiler. Unfortunately i am stuck in the early steps itself. To start, I am trying to run just a simple command line below, before i explore other advance options for pathway analys ...
rna-seq written 6 months ago by nsmaan10
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Comment: A: How to map and visualize differentially expressed genes on KEGG pathways
... Liux, Others: My GE file (data.txt) has identification columns such as, ENTREZID, Genename, etc. and i also have logFC and pvalue and padj, for each gene. Could someone please give me headstart on how to use KeggExp, using this file? Thank you ...
written 6 months ago by nsmaan10
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Comment: C: enhancedvolcano plot rowname question
... This is very cool. I am playing around with these options now for the best view. Thanks. Though I noticed one more thing that i am not sure how to correct: In the script, if i toggle the drawConnectors as TRUE or FALSE (everything else same), I get lot more labeled genes in TRUE. My aim is to only h ...
written 6 months ago by nsmaan10
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Comment: C: enhancedvolcano plot rowname question
... Embarrassed. Script working well now. Also, out of curiosity, is it possible to change just the 'labeled genes' as something different (for e.g., as filled markers or larger size markers). Thanks for all your help! ...
written 6 months ago by nsmaan10
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Comment: C: enhancedvolcano plot rowname question
... Yes. Gene was a factor. Working now. Still the script is showing error in reading object 'res2log2FoldChange' I modified it as: res2 <- read.table("results.txt", header=TRUE) res2$Gene <- as.character(res2$Gene) keyvals <- rep('black', nrow(res2)) names(keyvals) <- ...
written 6 months ago by nsmaan10 • updated 6 months ago by Kevin Blighe47k

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