User: kjo

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kjo30
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Posts by kjo

<prev • 21 results • page 1 of 3 • next >
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What's the relationship between "design" and "contrasts"?
... The explanations I've heard of "design" and "contrasts" make them sound like "overlapping"/non-independent concepts.  I.e. it would be possible to give values to these two parameters that are inconsistent with each other. Is that the case?  Or can the two parameters be specified completely independ ...
deseq2 written 12 months ago by kjo30 • updated 12 months ago by Ryan C. Thompson6.2k
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Comment: C: Where is the source code for qAbundanceDist?
... Thanks for the clarification. ...
written 16 months ago by kjo30
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Where is the source code for qAbundanceDist?
... The source code provided with the voom paper uses a function called qAbundanceDist, which gets loaded through the load statement shown below: > ls() [1] "" > load(url("http://bioinf.wehi.edu.au/voom/qAbundanceDist.RData")) > ls() [1] "qAbundanceDist" > class(qAb ...
voom written 16 months ago by kjo30 • updated 16 months ago by Gordon Smyth32k
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How to simulate count data to test rnaseq analysis code?
... All the rnaseq data simulation stuff I've found seems to be based on simulating reads, and applying a full analysis stack to those simulated reads. I'd prefer to simulate the counts matrix directly. Is there a package to generate synthetic counts data for testing/comparing rnaseq analysis software ...
rnaseq_analysis written 16 months ago by kjo30 • updated 16 months ago by Gordon Smyth32k
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How to compute "second-order" differences
... This is another hypothetical/toy example. I have 3 samples, corresponding to one untreated condition and two treated ones, as encoded in the metadata table below: > metadata drug 1 NONE 2 A 3 B Now, I create two deseq datasets, with different designs: dd ...
deseq2 written 16 months ago by kjo30 • updated 16 months ago by Michael Love15k
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On the relationship between design and contrasts
... This is a radically simplified version of: earlier question of mine.  (After I read the comments and answers that earlier post received, I realized that my query had conflated several different questions, which made it pretty confusing.  In this post I attempt to narrow the focus to only one questio ...
deseq2 written 16 months ago by kjo30 • updated 16 months ago by Ryan C. Thompson6.2k
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Comment: C: Confused by "composite" designs
... Thank you for your answer. Following up on your last suggestion, first I want to clarify that the factor called condition in my original post was meant to be exactly equivalent to the new one you propose, drugxdose. IOW, two rows in the augmented_metadata table have the same value in the condition ...
written 16 months ago by kjo30
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Answer: A: Confused by "composite" designs
...                                   ...
written 16 months ago by kjo30
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Comment: C: Confused by "composite" designs
...                             ...
written 16 months ago by kjo30
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Comment: C: Confused by "composite" designs
... For each k, the observations with replicate=k are related in that they refer to cells coming from the same batch.  IOW, each replicate represents a batch of cells that were grown together, then split into wells, and treated with a particular combination of drug and dose. For this question, it is OK ...
written 16 months ago by kjo30

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