User: bekah

gravatar for bekah
bekah10
Reputation:
10
Status:
New User
Location:
Last seen:
4 weeks, 1 day ago
Joined:
1 year, 6 months ago
Email:
r****@aber.ac.uk

Posts by bekah

<prev • 36 results • page 1 of 4 • next >
0
votes
1
answers
155
views
1
answers
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 5 weeks ago by bekah10
0
votes
0
answers
49
views
0
answers
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 6 weeks ago by bekah10
0
votes
1
answers
142
views
1
answers
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 6 weeks ago by bekah10
0
votes
1
answers
142
views
1
answers
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 6 weeks ago by bekah10
0
votes
1
answers
142
views
1
answers
Comment: C: WGCNA: Understanding module-trait correlations
... cheers! :) took me a while. but glad I got there!  ...
written 6 weeks ago by bekah10
0
votes
1
answers
142
views
1
answers
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 6 weeks ago by bekah10
0
votes
1
answers
155
views
1
answers
Comment: C: Pre-filtering genes counts vs normalised counts DESeq2
... Cheers for clearing up my confusion! ...
written 6 weeks ago by bekah10
0
votes
1
answers
155
views
1
answers
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 7 weeks ago by bekah10
0
votes
0
answers
82
views
0
answers
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 7 weeks ago by bekah10
0
votes
1
answers
108
views
1
answers
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 7 weeks ago by bekah10

Latest awards to bekah

Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 not installing

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 312 users visited in the last hour