User: fawazfebin

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fawazfebin30
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Posts by fawazfebin

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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 12 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 12 months ago by fawazfebin30 • updated 12 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 12 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 12 months ago by fawazfebin30
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... Great thanks ! ...
written 12 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... Yes, Sir. Great thanks. ...
written 12 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 12 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 13 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... > colnames(design.DEX) [1] "control" "resistant.2hr" "resistant.4hr" > DEX.contrasts Contrasts Levels resistant.2hrvscontrol resistant.4hrvscontrol control -1 -1 resistant.2hr 1 ...
written 13 months ago by fawazfebin30

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