User: Peter Langfelder

gravatar for Peter Langfelder
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Posts by Peter Langfelder

<prev • 194 results • page 1 of 20 • next >
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Comment: C: RNseq data for WGCNA
... The link to data is invalid (box reports the file has been removed or is unavailable). Plot a sample tree from the "Expr" data; you may have a monstrous batch effect. I hope the raw counts are really raw counts, not some transformed version. Your filter seems too stringent to me, I would filter on ...
written 3 days ago by Peter Langfelder1.3k
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Answer: A: RNseq data for WGCNA
... It is impossible to diagnose issues with your data or analysis without seeing the data (the code looks reasonable but it obviously isn't complete). One usually sees at least a few distinct branches in WGCNA analysis of expression data, but again, without knowing what your data represent and seeing t ...
written 4 days ago by Peter Langfelder1.3k
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Answer: A: WGCNA connecting trait data
... Add a "drop = FALSE" to this line: datTraits = allTraits[traitRows, -1] datTraits = allTraits[traitRows, -1, drop = FALSE] Your allTraits contains only 2 columns; when you remove the first one, you are left with just one column and R converts that into a single vector unless you add the drop = FAL ...
written 4 days ago by Peter Langfelder1.3k
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Answer: A: WGCNA works on time course data
... It depends on what your research aims/questions are. However, since you only seem to have a total of 7*4=28 samples, I would construct one network from all samples. If you find that the largest driver of variability is uninteresting, adjust the data for it and construct a new network. ...
written 5 weeks ago by Peter Langfelder1.3k
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BiocGenerics paste strange behavior (bug?)
... Not sure if I'm missing something here or whether this is a bug. The paste generic defined in BiocGenerics seems to behave weirdly when 'lapply'd to a list of character vectors. A simple example follows: Starting from a fresh R session: library(BiocGenerics) aa = list(letters[1:10], letters[11:20 ...
biocgenerics written 5 weeks ago by Peter Langfelder1.3k
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Answer: A: WGCNA - module membership preservation for low count genes
... This is a research project (which you will hopefully solve) and we won't be able to give you a solution. I suspect that the ability to reliably cluster a gene would depend on two things: its counts (WGCNA doesn't work all that well with low counts) and the number of 0 values the gene has. In single ...
written 8 weeks ago by Peter Langfelder1.3k
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Comment: C: DESeq function taking too long
... Does this happen while you run DESeq on the large data that was causing you trouble? If so, it would seem that swapping is not a problem, in which case I defer further solutions to Michael Love. ...
written 8 weeks ago by Peter Langfelder1.3k
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Answer: A: DESeq function taking too long
... Disclaimer: I am not  a Windows user so my advice may be off the mark, but here it goes anyway. You should be able to find that in the Resource Monitor, Memory tab. I think you should look at the "Hard faults per second" and the overall RAM utilization (see discussion here: https://superuser.com/qu ...
written 8 weeks ago by Peter Langfelder1.3k
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Answer: A: DESeq function taking too long
... Your "out of memory" error would suggest your RAM nearly exhausted.  What system are you on? Can you monitor your use of system resources, especially whether your computer needs to use swapping to disk? It may be that you run of physical RAM and the system starts swapping to disk, which causes the c ...
written 8 weeks ago by Peter Langfelder1.3k
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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 9 weeks ago by Peter Langfelder1.3k

Latest awards to Peter Langfelder

Scholar 7 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: WGCNA - Signed vs signed hybrid networks
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA - Signed vs signed hybrid networks
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA distance measures, clustering with TOM based on adjacency matrix type = "d
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA - signedKME function
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 19 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Theoretical WGCNA Question
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Theoretical WGCNA Question
Centurion 21 months ago, created 100 posts.
Scholar 23 months ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?
Scholar 3.0 years ago, created an answer that has been accepted. For A: WGCNA: overlapping colors in plotDendroAndColors?

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