User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 179 results • page 1 of 18 • next >
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Answer: A: WGCNA multiple data sets overlapping analysis
... For pairwise matching, use the function matchLabels. You will want to select one of the three sets as a reference set and match the labels of the other two sets to the reference.   ...
written 8 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA export to cytoscape
... Your reading of the code is incorrect. The code applies as.dist(), not dist(), to the input adjacency matrix (which is usually TOM). as.dist turns a matrix into distance representation by flattening the lower triangle. The information (e.g., numbers) remain exactly the same.  I'm not so sure about ...
written 10 days ago by Peter Langfelder1.2k
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Comment: C: WGCNA crashes R on OSX
... Neither WGCNA nor fastcluster (not hclust - that's a function within fastcluster) are Bioconductor packages...  so this may not be the right forum. ...
written 6 weeks ago by Peter Langfelder1.2k
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Answer: A: WGCNA: Different Detect Cut Heights Across Multiple Blocks
... I don't recommend setting the cutting arguments differently for each block (it is also not an option in standard WGCNA blockwiseModules). If you are concerned about apparently distinct branches being lumped into a single module, you can (1) decrease mergeCutHeight (this should also get rid of module ...
written 6 weeks ago by Peter Langfelder1.2k
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Comment: C: WGCNA exporting for Visant visualization
... I made a mistake in my code: instead of select = colnames(modTOM %in% IGFs) I should have written select = colnames(modTOM) %in% IGFs selectTOM = modTOM[select, select] Make sure you get something, e.g., type dim(selectTOM) and check that the result makes sense. The error suggests that your va ...
written 7 weeks ago by Peter Langfelder1.2k
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Comment: C: WGCNA exporting for Visant visualization
... You have to subset the modTOM matrix, not just set its dimnames. If IGFs contains the IDs of the genes you want to keep, I would do something like select = colnames(modTOM %in% IGFs) selectTOM = modTOM[select, select] then use selectTOM as input to the export function. ...
written 7 weeks ago by Peter Langfelder1.2k
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Answer: A: WGCNA exporting for Visant visualization
... If you know the genes you want to be exported, put their Entrez IDs in a vector, subset the adjMat argument to just those genes that are in the vector of desired gene IDs. This can be done instead of the restriction to a particular module. ...
written 7 weeks ago by Peter Langfelder1.2k
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Answer: A: understanding the meaning boxplot
... From help(boxplot.stats):       The two ‘hinges’ are versions of the first and third quartile,      i.e., close to ‘quantile(x, c(1,3)/4)’.  The hinges equal the      quartiles for odd n (where ‘n <- length(x)’) and differ for even      n.  Whereas the quartiles only equal observations for ‘n % ...
written 9 weeks ago by Peter Langfelder1.2k
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Comment: C: WGCNA error in network construction ?
... Dear Muhammad, there is no object Expr, you need to use datExpr. It seems that you are new to R and possibly to larger-scale computation and you may benefit from learning more about R and finding someone local who can guide you through some of the pitfalls. You seem to be using an R installation wh ...
written 10 weeks ago by Peter Langfelder1.2k
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Answer: A: Problem about picking soft threshold power in WGCNA software
... Please read the WGCNA FAQ, particularly point 6. You can use the default power  of 12 since you have hundreds of samples, but do make sure you don't have strong uninteresting sources of variation as described in the FAQ. ...
written 11 weeks ago by Peter Langfelder1.2k

Latest awards to Peter Langfelder

Scholar 3 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 13 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 17 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.7 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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