User: dennism9251

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Posts by dennism9251

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Comment: C: too few replicates to observe statistically significant differences
... Thank you for the advice, and yes that would be the design. ...
written 3 months ago by dennism92510
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too few replicates to observe statistically significant differences
... All my p-adj values are 1 when I call results and contrast "C" and "U." I am guessing that I have too few replicates (3 technical replicates) to observe statistically significant differences. In my PCAplot the samples were clustered (rather closely I may add) by sample rather than treatment which ma ...
deseq2 written 3 months ago by dennism92510 • updated 3 months ago by Michael Love26k
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Comment: C: Questions for ResultsNames() and the Contrast function
... Would your answer remain true, if you were to remove the interaction term? ...
written 3 months ago by dennism92510
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Comment: C: Questions for ResultsNames() and the Contrast function
... My apologies i mistyped it an meant DEG for differential gene expression ...
written 3 months ago by dennism92510
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Comment: C: Questions for ResultsNames() and the Contrast function
... Thank you for the reply, but all the questions except for 2b are referring the webpage I linked. As for 2b I wasn't too sure on what order I wanted the design in (you gave a reply to this question in my previous post). However, for clarification here would be my design. #design for question 2b ...
written 3 months ago by dennism92510
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Comment: C: Importance of Order in Design Formula
... Thank you for your answer, but the focus of this question isn't really results() or choosing the correct resultsNames/ contrast. I was wondering if calling results( *same contrast/name/etc* ) on two DESeqDataSets with differing design order would change the outcome. To clarify my question... de ...
written 3 months ago by dennism92510
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Questions for ResultsNames() and the Contrast function
... After reading [this post][1] and [this page][2] I would like some clarification for results(). For exemplification, I am will be referring to the webpage. **1a)** In "Example 1 : two-group comparison" what would be the difference between the following codes? results(dds, contrast=c("condition" ...
deseq2 written 3 months ago by dennism92510 • updated 3 months ago by Michael Love26k
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Comment: C: Importance of Order in Design Formula
... Also the design matrix does not change when specifying different orders in model.matrix() ...
written 3 months ago by dennism92510
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Importance of Order in Design Formula
... Can someone just quickly clarify if order matters when deciding on your design formula? In [this post][1] Anderson nicely explains that the design below is "Effect of treatment, accounting for the sample pairing" ~ Patient.ID + Treatment But I thought that variables included in your design tab ...
deseq2 written 3 months ago by dennism92510 • updated 3 months ago by swbarnes2340
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Deciphering Wilkinson Notation and Predictor Variables
... Trying to understand how to make the correct design for DESeq. [This very nice website][1] deciphers the notation for me, but I have no idea on how to interpret the predictor variables. After some fruitless google searches I was wondering if anyone here could lend out a helping hand by either linkin ...
deseq2 written 4 months ago by dennism92510 • updated 4 months ago by Michael Love26k

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