User: fawazfebin

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fawazfebin30
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12 months ago
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Posts by fawazfebin

<prev • 42 results • page 2 of 5 • next >
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Comment: C: Analysis of pathways using edgeR
... Yes Sir, I had used the same DGElist object and the same contrast used in DE analysis here..but couldnt understand why the error came still..Thanks ...
written 6 months ago by fawazfebin30
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Comment: C: Analysis of pathways using edgeR
... Thank you for the valuable guidance ,Sir. Is 'y' the DGElist object in the last command of fry test ? I get the following error while running it : > fry(y.DEX, index=HSA0420, design=design.DEX, contrast="ResistantvsControl.2hr") Error in .zscoreDGE(y = y, design = design, contrast = contrast) : ...
written 6 months ago by fawazfebin30
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Analysis of pathways using edgeR
... Hi I was analysing public RNA-Seq datasets from GEO for arriving at the most affected pathways /GO terms using the edgeR program. My objective was to determine whether Ca signalling pathway had a considerable effect in the corresponding phenotype. I did a DE analysis with edgeR and arrived at resul ...
rnaseq edger kegg differential expression written 6 months ago by fawazfebin30 • updated 6 months ago by Gordon Smyth35k
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R code for finding wobble/redundant positions in an RNA string
... Hi Can anyone help me to code for finding the positions in an RNA string , where even if we change the nucleotide there remains no change in the resulting amino acids. I would prefer to code in R. The output needs to list the positions in the strings where the changes can be made. The RNA string do ...
R rna code wobble written 7 months ago by fawazfebin30
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Answer: A: read.delim taking infinite time in edgeR analysis
... Great thanks Aaron ! Shall check on it. ...
written 7 months ago by fawazfebin30
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read.delim taking infinite time in edgeR analysis
... Hi I was using the read.delim function on a gene counts file to construct a table of gene counts for six samples for performing edgeR differential expression analysis. The input counts file (27.4 MB file) is in the ~/ directory. But the command seems running for an infinite time with no return of R ...
edger read.delim written 7 months ago by fawazfebin30
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TCGAvisualize_EAbarplot error in TCGAbiolinks
... Hi  I was trying to visualise the bar plot for enrichment analysis using  following command in TCGAbiolinks but arrived at " null device" . > TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP), + GOBPTab = ansEA$ResBP, + GOCCTab = ansEA$ResCC, + ...
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Error in move(i, file.path(path, i)) : I could not find the file: 95a5d709-7454-4f76-84b0-a505c32baeb5 ; GDCdownload error
... Hi I was analysing TNBC datasets from TCGA using TCGAbiolinks . The following error was obtained while downloading the data : > GDCdownload(query = queryDown, + directory = DataDirectory) Downloading data for project TCGA-BRCA GDCdownload will download: 1.844745499 GB Executing GDC ...
tcgabiolinks gdcdownload tcga-brca written 8 months ago by fawazfebin30
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Comment: C: GDCdownload error in TCGAbiolinks: Invalid zip name argument
...   I get the following error while installing from GitHub: > devtools::install_github('BioinformaticsFMRP/TCGAbiolinks') Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master Installing TCGAbiolinks In ...
written 9 months ago by fawazfebin30
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Comment: C: GDCdownload error in TCGAbiolinks: Invalid zip name argument
... Great thanks! ...
written 9 months ago by fawazfebin30

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