User: philip.freda

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Posts by philip.freda

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Comment: C: How do I discern if a magnitude difference in expression is up-regulation in one
... even if the expression in adults remains unchanged from constitutive levels, which I have as part of my data set as a control ...
written 10 months ago by philip.freda0
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Comment: C: How do I discern if a magnitude difference in expression is up-regulation in one
... But if larvae down regulate the gene, it will appear positive in the comparison. I've seen it multiple times ...
written 10 months ago by philip.freda0
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Comment: C: How do I discern if a magnitude difference in expression is up-regulation in one
... Nope, just two groups. Perhaps what I did not express very well is no expressional activation in one group and down regulation in the other looks like upregulation in the first group when it isn't as all comparisons are adult - larvae. Therefore a positive LogFC just means adults have higher express ...
written 10 months ago by philip.freda0
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How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
... When exporting TopTags in EdgeR, you of course get LogFC which have a sign associated with them and that refers to which group has higher expression but it doesn't really tell you anything about in which group the gene is significantly up-regulated in. An example would be a LogFC of 3.5. This would ...
edger R differential gene expression gene list up-regulation written 10 months ago by philip.freda0 • updated 10 months ago by Gordon Smyth37k
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Comment: C: EdgeR model not of full tank
... Another question: does renumbering them still keep them separate? In other words line 1 in LL and line 1 in HL are two totally different genetic lines ...
written 24 months ago by philip.freda0
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Comment: C: EdgeR model not of full tank
... Here is the new model matrix:   (Intercept) phenoL0LL phenoL0LL:lineL0380 phenoL0HL:lineL0441 phenoL0LL:lineL0486 phenoL0HL:lineL0832 phenoL0HL:lineL0913 droso_1_exp_count 1 1 0 0 0 0 0 droso_14_exp_count 1 1 1 0 0 ...
written 24 months ago by philip.freda0
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Comment: C: EdgeR model not of full tank
... I tried what you proposed but got this error. Any idea what the problem may be? The error is much shorter than previously with only one line (913) listed within the error   Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05,  :    Design matrix not of full rank.  The follo ...
written 24 months ago by philip.freda0
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EdgeR model not of full rank
... I have data that has genetic line (line) and phenotype (pheno) as my factors and my data looks something like this: sample_id line rep pheno 1 358 1 LL 3 358 2 LL 14 380 1 LL 15 380 2 LL 25 441 ...
edger model rank written 2.0 years ago by philip.freda0

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