User: bekah

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bekah20
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1 year, 8 months ago
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r****@aber.ac.uk

Posts by bekah

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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 3 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 3 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 3 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 3 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 3 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 3 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 3 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 3 months ago by bekah20
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ClusterProfiler - enrichKEGG on specific pathways
... Hiya, I have blasted the genes of my non-model organism using the KEGG blastKOALA - so have a list of k numbers associated with my genes. I am using clusterprofiler to run enrichment to see which pathways are significantly enriched. I tried against mze, but it said no genes could be mapped, so I t ...
clusterprofiler kegg enrichkegg written 3 months ago by bekah20
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Comment: C: KEGG enrichment for non-model
... I realised that GAGE is not suitable for my data - as I am using KO so, multiple genes that are similar have been given the same k number which makes assigning the correct LFC difficult. What I was wanting was a software that used enrichment test on keggIDs rather than expression data - so I have us ...
written 3 months ago by bekah20

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Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2 not installing

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