User: reara

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reara10
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Posts by reara

<prev • 12 results • page 1 of 2 • next >
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Gene expression variability
... Hi, I have a RNA-Seq gene expression matrix with rows as genes and columns as samples. Please let me know how I would go about finding the genes with the highest variability? ...
gene next-gen rna-seq written 4 days ago by reara10 • updated 4 days ago by Nicolas Rosewick9.0k
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WGCNA Intramodular Connectivity
... Hi everyone-Im having some trouble with figuring out what value to use for the "colors" argument below. Im following the standard Horvath tutorial. I tried using the "moduleColors" as the argument but it does not seem to be working: adjMat = adjacency(datExpr, selectCols = NULL, ...
wgcna next-gen rna-seq R written 13 days ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... > Just following the Horvath standard tutorial: datExpr0 = as.data.frame(t(femData[, -c(1:8)])); names(datExpr0) = femData$substanceBXH; rownames(datExpr0) = names(femData)[-c(1:8)]; # Plot a line to show the cut abline(h = 7, col = "red"); # Determine cluster under ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... Thank you so much-I did try that before and this is the code and output since mine is an unsigned network. How would I find out the actual genes from below result in a tabular format: intramodularconnectivity = intramodularConnectivity.fromExpr(datExpr, moduleColors, ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... ok so could you confirm what my input matrix should be? ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... haha The Cave is where it all happens, to be sure. Yes you are absolutely right with the moduleEigengenes which was the first thing I tried. However, it only gives the 1st PC which is an abstract value. I want the actual genes (and their values of course) that contribute to give that abstract value. ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... Ah I see-which one, though? We have a quite a few with a similar trajectory. Anyone else who you might be able to suggest? ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... Thank you, Kevin. Would your package help me identify and extract which genes in a module contribute to the Eigengene? ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... > The Principle Components analysis must have the genes factors, and you'd have to pick out the ones with max absolute value coefficient. Could you clarify the above line? How would I go about doing that? ...
written 4 weeks ago by reara10
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Comment: C: Extracting Genes that contribute to 1st PC
... `eigenmatrix.black.na <- t(na.omit(t(eigenmatrix.black))) df_black <- read.csv('eigengmatrix.black.na.csv', header = TRUE) X_black <- df_black X_black <- as.matrix(df_black) nPC=1 n=dim(X_black)[1] p=dim(X_black)[2] svd1 = svd(X_black, nu = min(n, p, nPC), nv = min(n, p, nPC)) s ...
written 4 weeks ago by reara10

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