User: Liz Fernandez

gravatar for Liz Fernandez
Reputation:
70
Status:
New User
Location:
Australia
Last seen:
4 years, 5 months ago
Joined:
7 years ago
Email:
l*********@gmail.com

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Posts by Liz Fernandez

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Expression of genes in module very different to representative eigenmodule expre
... Hi Marge,  As I said in my response to Devon I ended up merging at a much lower threshold (0.1), which effectively resulted in only in three eigengenes merging (tan, brown and salmon in the dendogram above). In fact I get very meaningful results with this approach. I do not have correlations to tra ...
written 4.6 years ago by Liz Fernandez70
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Comment: C: Expression of genes in module very different to representative eigenmodule expre
... Thanks for the suggestion! I tried lowering the threshold to 0.1 and, although the eigengene expression is very similar between clusters that were previously merged (as expected) I get much more informative Gene Ontology enrichments for each module and concordant gene expression heatmaps.  I was cu ...
written 4.7 years ago by Liz Fernandez70
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Answer: A: WGCNA implementation for differential co-expression analysis
... The authors recommend against using DE data. Here is the note from the WGCNA website: "We do not recommend filtering genes by differential expression. WGCNA is designed to be an unsupervised analysis method that clusters genes based on their expression profiles. Filtering genes by differential expr ...
written 4.7 years ago by Liz Fernandez70
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Expression of genes in module very different to representative eigenmodule expression (WGCNA)
... I am using WGCNA for the first time to identify gene co-expression modules across a time course with 40+ samples (RNA-Seq). I’ve removed lowly expressed genes and focused the analysis on the 15,000 most dynamically expressed genes. The free-scale topology and other indicators (sample clustering, etc ...
wgcna network gene expression rna-seq written 4.7 years ago by Liz Fernandez70 • updated 16 months ago by Brawni100
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Comment: C: How To Generate "Ucsc Genes Track" In Local Ucsc Genome Browser?
... Thanks! This is what I want to do but I would also like to add links to the mRNA, peptide, Uniprot, etc, in the help page. I believe this can be done with linked SQL tables but I'm not sure what is the best way to go about generating the tables and linking them correctly. ...
written 6.3 years ago by Liz Fernandez70
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Comment: C: How To Generate "Ucsc Genes Track" In Local Ucsc Genome Browser?
... I want to generate the first one, both the help page and the track behind all that information (knownGene). I already have the positions and annotations ready. Sorry about the wrong link. ...
written 6.3 years ago by Liz Fernandez70
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How To Generate "Ucsc Genes Track" In Local Ucsc Genome Browser?
... Hi all, I would like to generate a "UCSC genes" track for a genome hosted in the our local UCSC browser. Something like this, with subsections and most data linking to an external url. I'm starting off from a tab delimited annotation file and I would like to end up with all data loaded onto SQL an ...
genome ucsc browser written 6.3 years ago by Liz Fernandez70 • updated 5.7 years ago by Biostar ♦♦ 20
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Comment: C: Is There A Fastq Alternative To Fastx_Collapser (Outputs Fasta)?
... This tool is great and real quick. I've looked at the code but couldn't find a good way to get also the name of the read with the highest average quality to be printed in the output (my C knowledge is fairly rusty). What I'm trying to do is to is to unique paired end reads so I need to know where on ...
written 6.8 years ago by Liz Fernandez70

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