User: Chris Gene

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Chris Gene60
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Posts by Chris Gene

<prev • 21 results • page 1 of 3 • next >
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Comment: A: GeneOverlap - overlap of DE genes from 2 or 3 RNA-Seq experiments
... How can I determine whether the overlap is statistically significant? Is there an enrichment? ...
written 16 months ago by Chris Gene60
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GeneOverlap - overlap of DE genes from 2 or 3 RNA-Seq experiments
... I am comparing 3 differentially expressed (DE) gene datasets. Ideally I would want to do a 3-way comparison, but breaking it down into pairwise would be fine too. As I understand, GeneOverlap functions in a way similar to a hypergeometric test, and does not take into account the background of genes ...
R hypergeometric test rna-seq geneoverlap written 16 months ago by Chris Gene60
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Comment: C: Time course experiments in DESeq2
... Thanks Mochael. That's very helpful. ...
written 18 months ago by Chris Gene60
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Comment: C: Time course experiments in DESeq2
... Thanks Michael. That's very helpful. ...
written 18 months ago by Chris Gene60
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Answer: A: Time course experiments in DESeq2
... Thank you Michael. I just realized I hadn't releveled the data at all. When performing a Wald test, I'm not sure whether I should include the contrast argument. As I understand from the documentation, if I provide the interaction term under name, and the contrast, the latter will take priority ...
written 19 months ago by Chris Gene60
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Time course experiments in DESeq2
... Hello, I'm having a hard time understanding the time course experimental work flow in DESeq2. I am using the F1000 paper as a template (Love MI, Anders S, Kim V and Huber W. RNA-Seq workflow: gene-level exploratory analysis and differential expression [version 1; referees: 2 approved]. F1000Research ...
htseq time course deseq2 multivariate rna-seq written 19 months ago by Chris Gene60
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Comment: C: DESeq2 inconsistent results
... When I reopened the session to get the session info as requeste, the error did not reproduce... I happened to update DESeq2 in the interim - i wonder whether that was it... ...
written 19 months ago by Chris Gene60
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DESeq2 inconsistent results
... I'm getting inconsistent numbers of genes from DESeq2 results. Using the default FDR, On summary(res), I have: out of 26572 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 2117, 8% LFC < 0 (down) : 1675, 6.3% (i.e., total `3792`) However, i ...
deseq2 rna-seq differential gene expression written 19 months ago by Chris Gene60 • updated 19 months ago by geek_y8.1k
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Answer: A: Using samtools and Picard tools with cram files
... Worked fine with the update, thanks. And picard's BamToFastq? I'm using v. 1.99, that already supports cram files, but still get parsing error: Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 1 Line: CRAM^C^@ (...) at net.s ...
written 19 months ago by Chris Gene60
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Comment: A: Using samtools and Picard tools with cram files
... It's 0.1.18; doesn't work with that option. I'll update and try again. Thanks! ...
written 19 months ago by Chris Gene60

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Popular Question 18 months ago, created a question with more than 1,000 views. For Batch effect in DESeq2 - multiple factor or SVA?

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