User: fawazfebin

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fawazfebin30
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Posts by fawazfebin

<prev • 43 results • page 1 of 5 • next >
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GDCprepare error in TCGAbiolinks
... Hi, I was trying to do a differential expression expression analysis using TCGAbiolinks. The tumour data was queried and downloaded using GDCquery and GDCdownload. The GDCprepare command gave the following error. >library(TCGAbiolinks) >query.colon.cancer <- GDCquery(project = "TCGA-COAD" ...
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Comment: C: Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... As simple as that :) .Great thanks, Sir.   ...
written 20 months ago by fawazfebin30
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(Closed) Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... Hi , Can anyone help me to separately list top up-regulated and down-regulated genes from the list of differentially expressed genes. Is there any command for the same? Thanks in advance. ...
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Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
... Hi , Can anyone help me to separately list top up-regulated and down-regulated genes from the list of differentially expressed genes. Is there any command for the same? Thanks in advance. ...
edger differential gene expression upregulated genes downregulated genes written 20 months ago by fawazfebin30 • updated 20 months ago by lisacarlon250
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Comment: C: Analysis of pathways using edgeR
... The row names of y.dex are Ensembl IDs . ...
written 20 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... > HSA0420 <- KEGG$GeneID[ KEGG$PathwayID=="path:hsa04020" ] > fry(y.DEX, index=HSA0420, design=design.DEX, + contrast=DEX.contrasts[,"resistant.2hrvscontrol"]) NGenes Direction PValue PValue.Mixed set1 0 Up NaN 0   Can the output of the above fry func ...
written 20 months ago by fawazfebin30
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... Great thanks ! ...
written 20 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... Yes, Sir. Great thanks. ...
written 20 months ago by fawazfebin30
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SPIA function error in ToPASeq
... Hi I was doing a pathway analysis of RNA-Seq data using ToPASeq program. I ran the following commands : > library("ToPASeq") > library("gageData") > DEXcounts = read.table("/home/febin/DEXcounts.txt", header = TRUE ,row.names = 1) > DEXcounts = DEXcounts[,6:ncol(DEXcounts)] > DEXco ...
spia R pathway analysis topaseq written 20 months ago by fawazfebin30
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Answer: A: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... Hi Great to know about the new package for pathway analysis. I installed the program from GitHub and ran the 'run_pathfindR' command on input ( a dataframe with gene symbols, logFC and adjusted p-values ) but got the following error: > result2hr = run_pathfindR(input.2hr) ## Testing input Err ...
written 20 months ago by fawazfebin30

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Popular Question 20 months ago, created a question with more than 1,000 views. For No genes found in universe : goana error

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