User: Adamc

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Adamc530
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Posts by Adamc

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Intersection of multiple methods for RNA-Seq differential expression: conservati
... > I would not even be looking at transcripts at the alpha 5% threshold. Are you referring to genes which are "borderline" significant? ...
written 25 days ago by Adamc530
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Comment: C: Intersection of multiple methods for RNA-Seq differential expression: conservati
... When I started with analysis of RNA-Seq data there was no clear consensus on what analysis approach was going to become the "gold standard"- both DESeq and EdgeR were new-ish, and it was not like with Affymetrix microarrays where Limma had been the clear choice for years. Hence, this sort-of weak en ...
written 25 days ago by Adamc530
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Comment: C: Intersection of multiple methods for RNA-Seq differential expression: conservati
... > It's mostly on the periphery of significance that you get discordant results Yes, the original intent was to increase stringency. Although both packages use the negative binomial, distribution, I've occasionally seen cases where DESeq2 and EdgeR assigned fold-changes that went in opposite dire ...
written 25 days ago by Adamc530
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Intersection of multiple methods for RNA-Seq differential expression: conservative or crazy?
... Hi, For a while now, I've been looking at the intersect of the significant results from DESeq2 and EdgeR as my standard for determining differentially expressed genes, treating EdgeR as a filter over the DESeq2 results. I usually report fold-changes from DESeq2 as the foldchange shrinkage when coun ...
differential-expression rna-seq written 26 days ago by Adamc530 • updated 26 days ago by Friederike820
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Forum: Bytes and Bio- Check out my first science communication video- looking for additional ideas
... Hi Biostars, I created a short video for a science communication contest a couple of months on "Big Data in Biology". I have been thinking of trying to turn this into a video series centered around demystifying bioinformatics and computational biology for those who might not have a background in th ...
bioinformatics forum datascience video written 8 weeks ago by Adamc530
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Answer: A: TCGA RNA-seq data, a simple question.
... Not all TCGA samples were sequenced in the same place, so it may vary depending on what type of tumor you're looking at. Check the papers that have been published from the TCGA. For example for Glioblastoma, "Nonstrand specific RNA sequencing performed at the Broad Institute uses a large-scale, aut ...
written 8 months ago by Adamc530
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Comment: C: Dream short-term teaching gig in Okinawa, Japan
... Just wanted to comment- I had the opportunity to visit OIST a few years ago. I think things were still getting started at that point, but it's a very impressive facility with a surprising array of resources on-site (which is important, since it's on a tropical island), including a large compute clus ...
written 9 months ago by Adamc530
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Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
... Hi, I have been working on an RNA-Seq dataset on which I applied RUVSeq (ruvr method) at the gene-count level to account for some unexpected variance before running DESeq2. I am also working on using DEXSeq to look at differential exon usage. Optimally, I would be able to also apply RUVSeq to the b ...
dexseq R bioconductor ruvseq rna-seq written 10 months ago by Adamc530
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Comment: C: WGCNA on gene abundance data
... Do you have counts for each sample then? Sorry, having a bit of trouble understanding your description. Are your values for gene counts derived from different sources (counts for gene A were derived from one publication, and for gene B from a different publication, etc)? I think a simpler clustering ...
written 17 months ago by Adamc530
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Comment: C: WGCNA on gene abundance data
... Hi, what sort of assay are your gene abundances derived from? How many genes are you looking at and how many samples do you have? Also, please put your code in a "code sample" block (available as a button with the 101 in the post editor) so that it's a bit easier to read here. ...
written 17 months ago by Adamc530

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Popular Question 7 months ago, created a question with more than 1,000 views. For Data management/annotation solutions for microarray and NGS experiments
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Popular Question 16 months ago, created a question with more than 1,000 views. For Finding miRNA & small RNA that are human-specific?
Popular Question 16 months ago, created a question with more than 1,000 views. For Validity Of Gene List Comparisons For Lists Originating From Different Platforms?
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Scholar 21 months ago, created an answer that has been accepted. For A: a question about some "basic numbers" for rna-seq experiments
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