User: paul.alto

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paul.alto50
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Posts by paul.alto

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Comment: C: Further clarification on when not to use duplicateCorrelation with technical rep
... Thank you for the clarification and for taking the time to answer my question! ...
written 8 weeks ago by paul.alto50
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Comment: C: Further clarification on when not to use duplicateCorrelation with technical rep
... Thanks for your reply, Aaron. You summary is very helpful. In the "Not-quite-technical replicates" scenario, my reasoning was the opposite from yours. I thought that if the replicates are expected to be similar, then I would treat them as "technical replicates" and if they are expected to be variabl ...
written 8 weeks ago by paul.alto50
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Comment: C: Further clarification on when not to use duplicateCorrelation with technical rep
... Thank you for your reply. In my case, if I don't have real technical replicates, should I still pool them (RNA-seq) or use `duplicateCorrelation`? ...
written 9 weeks ago by paul.alto50
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Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
... After reading the limma manual and paper and several posts about using `duplicateCorrelation` with technical replicates mixed with biological replicates, I am still unsure when to use it (and why not use it). The 2015 limma paper says about `duplicateCorrelation`: "More generally, the same idea is ...
limma duplicatecorrelation rna-seq technical replicates biological replicates written 9 weeks ago by paul.alto50 • updated 8 weeks ago by Aaron Lun25k
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Comment: C: What's the best way to use "semi" technical replicates with biological replicate
... Makes sense, I'll make sure to downsample before summation. Thank you so much! ...
written 8 months ago by paul.alto50
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Comment: C: What's the best way to use "semi" technical replicates with biological replicate
... Thank you very much, Aaron! Extremely helpful, as usual! I should have mentioned that the experiment is RNA-seq. Would averaging samples still be a solution or would it violate the count data assumptions? I understand your point about cell lines not being proper replicates. I have been considering t ...
written 8 months ago by paul.alto50
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What's the best way to use "semi" technical replicates with biological replicates?
... I have a question about how to analyze a mix of biological and semi-technical replicates. The experiment I am analyzing consists of 3 cell lines X 3 replicates of each cell line X 2 conditions. The 3 replicates are done with the same cell line, but independently treated, processed and sequenced, so ...
limma technical replicates paired analysis biological replicates written 8 months ago by paul.alto50 • updated 8 months ago by Aaron Lun25k
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Comment: C: contrast design of DESeq2 for correlated data
... You are right, I have control and treatment for each replicate and cell line. I have been using ~cell + condition, but I just wanted to make sure I shouldn't be doing something else, so thanks for the clarification. For others reading this thread in the future, this is the design I have: sample ...
written 20 months ago by paul.alto50
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Comment: C: contrast design of DESeq2 for correlated data
... Hi, Michael, first of all thanks a lot for helping DESeq2 users! Regarding the correlation between samples from the same individual, do you think that it is always necessary to duplicateCorrelation() and limma? How well do you think DESeq2 performs when there are correlated samples that are not str ...
written 20 months ago by paul.alto50
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Comment: C: Differential expression due to extreme outliers in DESeq2
... Thanks for the suggestion, Mike. Now that gene has pvalue = 0.31 and padj = 0.58. Another gene that had the same problem also has higher padj. ...
written 24 months ago by paul.alto50

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