User: fawazfebin

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fawazfebin30
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Posts by fawazfebin

<prev • 42 results • page 1 of 5 • next >
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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 3 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 3 months ago by fawazfebin30 • updated 3 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 3 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 3 months ago by fawazfebin30
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Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... Great thanks ! ...
written 3 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... Yes, Sir. Great thanks. ...
written 3 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 3 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 4 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 4 months ago by fawazfebin30

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