## User: paul.alto

paul.alto50
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#### Posts by paul.alto

<prev • 18 results • page 1 of 2 • next >
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... Thank you for the clarification and for taking the time to answer my question! ...
written 4 days ago by paul.alto50
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... 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 5 days ago by paul.alto50
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... 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 10 days ago by paul.alto50
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... 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 ...
written 11 days ago by paul.alto50 • updated 6 days ago by Aaron Lun25k
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... Makes sense, I'll make sure to downsample before summation. Thank you so much! ...
written 6 months ago by paul.alto50
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... 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 6 months ago by paul.alto50
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... 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 ...
written 6 months ago by paul.alto50 • updated 6 months ago by Aaron Lun25k
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... 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 18 months ago by paul.alto50
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... 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 18 months ago by paul.alto50
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... 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 22 months ago by paul.alto50

#### Latest awards to paul.alto

Teacher 16 months ago, created an answer with at least 3 up-votes. For A: about SVA: matrix of corrected expression values

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