User: bekah

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bekah20
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4 months, 4 weeks ago
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2 years, 4 months ago
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r****@aber.ac.uk

Posts by bekah

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Module preservation WGCNA
... Hi, sorry for the delay in responding I have just moved house! Thank you very much, I will try this ASAP! ...
written 7 months ago by bekah20
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Module preservation WGCNA
... Hi, I have a single network that I have created using WGCNA, is it possible to test module preservation on just the one network. I tried using the following: #FOR MODULE PRESERVATION data=read.csv("preservation.csv", header=TRUE) # expression data file, with columns = genes and rows = samples mo ...
wgcna modulepreservation wgcna package written 7 months ago by bekah20 • updated 7 months ago by Peter Langfelder2.1k
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Comment: C: Pre-filtering genes counts vs normalised counts DESeq2
... Hi Michael, If I filter out a readcount of less than 50 for row sums dst27<- dst27[rowSums(counts(dst27))>=50,] I get a slightly higher number of DEG with padj<0.05 than when filtering with dst27<- dst27[rowSums(counts(dst27))>10,] Is this still a valid filter or am I undermining ...
written 11 months ago by bekah20
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Use of bicor in WGCNA
... Hi, I am confused about when the bicor and its options should be specified. I have 20 samples, normalised expression data and a traits file containing binary traits (e.g. 0=uninfected, 1=infected). The literature suggests that bicor should be used over pearsons for robustness, but that MaxPOutliers ...
wgcna bicor wgcna package written 11 months ago by bekah20
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Comment: C: WGCNA: Understanding module-trait correlations
... Thank you for your response, I have just tried the bicor within the pick soft threshold and my soft threshold does not reach 0.85, so i will stick to pearsons - the reason I swapped to bicor was from the FAQ section of WGCNA recommending its use and against pearsons due to outlier sensitivity - but ...
written 11 months ago by bekah20
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Comment: C: WGCNA: Understanding module-trait correlations
... Sorry another quick question - in the tutorial document, https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.pdf the only place I can see signed specified is on the axis label of the soft threshold graph? Does this mean that the defa ...
written 11 months ago by bekah20
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Comment: C: WGCNA: Understanding module-trait correlations
... cheers! :) took me a while. but glad I got there!  ...
written 11 months ago by bekah20
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Comment: C: WGCNA: Understanding module-trait correlations
... Sorry for the delay, I've been trying to get my head around the unsigned, signed and hybrid analysis. So - unsigned - negative and positive correlations between expression values of the genes are all treated equally whether negative or positive? - signed - negative correlations between expression va ...
written 11 months ago by bekah20
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Comment: C: Pre-filtering genes counts vs normalised counts DESeq2
... Cheers for clearing up my confusion! ...
written 11 months ago by bekah20
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Comment: C: Pre-filtering genes counts vs normalised counts DESeq2
... Hi Michael, I have now read several posts on pre-filtering and have confused myself. I understand that pre-filtering isn't necessary when using DESeq2 due to the filtering step that occurs in the DESeq function. I have the script for comparing across 20samples for removing the genes with v low cou ...
written 11 months ago by bekah20

Latest awards to bekah

Popular Question 7 months ago, created a question with more than 1,000 views. For WGCNA: Understanding module-trait correlations
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 not installing

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