User: mart1139

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mart11390
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Posts by mart1139

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GOseq No Underrepresented Categories
... Hi All, I am using GOseq as part of the Trinity pipeline to perform gene ontology testing for genes in a de novo transcriptome assembly. I used edgeR to perform DGE analysis comparing groups that were treated with a chemical to those that went untreated, and my output looks like the following: &g ...
goseq go enrichment written 14 months ago by mart11390
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Comment: C: Building contrasts for combined treatment groups to compare to a control
... Just wanted to confirm the point you made in your P.S. statement -- If I want to test the null hypothesis within a given population given the contrasts below: my.contrasts <- makeContrasts(lm_cvt=(lm_th+lm_tl)/2-lm_c, lc_cvt=(lc_th+lc_tl)/2-lc_c, ct_cvt=(ct_th+ct_tl)/2-ct_c, levels=design) I c ...
written 16 months ago by mart11390
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Comment: C: Building contrasts for combined treatment groups to compare to a control
... Thanks Aaron, I see my mistake with the first set of contrasts now. Also, your explanation of the effects of increasing library size on standard error and power to detect DE genes was extremely clear and much appreciated. I was concerned that the all population had nearly 2 orders of magnitude more ...
written 16 months ago by mart11390
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Building contrasts for combined treatment groups to compare to a control
... Hello, my name is Alex and I am currently a graduate student at Purdue University. I am using edgeR to conduct differential gene expression for a project wherein I'd like to compare 3 treatment groups [control (c), treatment-low (tl), and treatment-high (th)] across 3 population groups (lm, lc, and  ...
edger design and contrast matrix written 16 months ago by mart11390 • updated 16 months ago by Aaron Lun24k
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Comment: C: edgeR - comparing treatment groups across multiple populations
... Great, that makes sense. I appreciate your help in clarifying this issue!  Best, Alex. ...
written 19 months ago by mart11390
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Comment: C: edgeR - comparing treatment groups across multiple populations
... Thanks for the quick response Aaron. I was definitely concerned that I might be missing out on DEGs by comparing each population in a separate model and this solution puts those worries at ease. When making the contrast to control all populations, I was planning on doing something like the following ...
written 19 months ago by mart11390
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edgeR - comparing treatment groups across multiple populations
... Hello, my name is Alex Martinez and I am currently a graduate student at Purdue University. I am using edgeR to conduct differential gene expression for a project wherein I'd like to compare 2 treatment groups (control versus treatment) across 3 population groups (lm, lc, and ct). After reading thro ...
rnaseq edger written 19 months ago by mart11390 • updated 19 months ago by Aaron Lun24k

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