User: David Requena

gravatar for David Requena
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20
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Location:
The Rockefeller University. New York, USA.
Website:
https://github.com/dav...
Last seen:
1 month, 2 weeks ago
Joined:
2 months ago
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d*******@rockefeller.edu

Posts by David Requena

<prev • 4 results • page 1 of 1 • next >
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Comment: C: About the results and contrast (DESeq2)
... Thanks a lot! David ...
written 8 weeks ago by David Requena20
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Answer: A: DESeq2 Design Formula for Time Series Experiment
... To compare time points, you should consider "timepoint" in your formula, as you did. To compare treated vs untreated, you should include "treatment" in your formula. If you think that your treated patients will experience changes over time, which are different than the changes experienced by the u ...
written 8 weeks ago by David Requena20
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Answer: A: About the results and contrast (DESeq2)
... Thanks a lot for your answer and recommendations! I get an error with the approach B: "Error in results(ds.deseq, contrast = c("sample_type", "metastasis", "primary"), : only list- and numeric-type contrasts are supported for user-supplied model matrices". So, I used this: res <- results(ds.de ...
written 8 weeks ago by David Requena20
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About the results and contrast (DESeq2)
... Hello! I want to make a differential expression analysis of some RNAseq data using DESeq2. Essentially, I have 3 types of tissue: normal, primary tumor and metastasis. These samples were sequenced in 4 groups and I found an evident batch effect (clusters by group processed, indicated in the variabl ...
deseq2 differential expression rna-seq written 9 weeks ago by David Requena20

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