User: Peter Langfelder

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Posts by Peter Langfelder

<prev • 185 results • page 1 of 19 • next >
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Answer: A: org.Rn,eg.db not yet available for R version 3.3.3
... Try again with org.Rn.eg.db instead of org.Rn,eg.db note the dot instead of comma...   ...
written 7 days ago by Peter Langfelder1.2k
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Comment: C: DESeq2: Error in cleanContrast
... Glad to be of help. Although this is not your (or DESeq2's) fault at all, it may be helpful to add some sort of a check inside your pipeline that factor levels are valid names. This type of a problem (factor levels that are not valid names) is probably quite common but it can be difficult for non-R- ...
written 12 days ago by Peter Langfelder1.2k
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Answer: A: DESeq2: Error in cleanContrast
... Your "MC" level of tissue is most likely actually "MC ". Note the space at the end. The telltale sign of this is the apparently uneven spacing of the levels in your outputs. The space is converted to a period (".") when column names are checked deep inside the DESeq2 analysis pipeline. Make sure the ...
written 12 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA: Exporting MEs with Subject/Sample Identification
... The simplest way to do it, assuming your expression data carry valid rownames: rownames(MEs) = rownames(datExpr) (replace datExpr with the object that carries our expression data). More generally, you can add a column to MEs that has sample ID, or multiple columns that have all the information y ...
written 16 days ago by Peter Langfelder1.2k
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Answer: A: WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped
... Thanks for the bug report. It is difficult to say what the problem is apart from the obvious conclusion that it happens somewhere in the compiled code of WGCNA calculations. Try installing the newest WGCNA version and see if the problem persists. ...
written 6 weeks ago by Peter Langfelder1.2k
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Answer: A: Intramodular connectivity RNA-seq WGCNA
... The code should work. RNA-seq, after suitable normalization and transformation, can be analyzed just any other data. You may want to look at the WGCNA FAQ, especially point 4. Then simply follow the WGCNA tutorials or the code in the book (which you seem to be following already).   ...
written 7 weeks ago by Peter Langfelder1.2k
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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 9 weeks 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 weeks 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 3 months 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 3 months ago by Peter Langfelder1.2k

Latest awards to Peter Langfelder

Scholar 5 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 15 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 17 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 19 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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