User: jcalis
jcalis • 10
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- Last seen:
- 7 months ago
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- 3 years, 2 months ago
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- j*****@rockefeller.edu
Posts by jcalis
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Thanks again!
I'll move on with the grouping as you suggested, I agree that it is always better to make something as easy (to follow) as possible.
Just to check whether something went wrong or not. Here is the way I selected the factors for each contrast, first by selecting factors for each grou ...
written 7 months ago by
jcalis • 10
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... Thanks a lot for your help.
I've been looking into how to implement your suggestions and came to the following. I'd like to share my current set-up
here, both to see if it is correct, and to help others facing the same problem.
Aside from the factors mentioned above, I now also include another c ...
written 7 months ago by
jcalis • 10
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... I would like to make several contrasts:
- disease vs healthy. For all tissues, and tissue specific (tissueA_disease - tissueA_healthy or tissueB_disease - tissueB_healthy)
- tissueA vs tissueB.
- Difference of differences contrast for disease vs healthy in one tissue vs the other: (tissueA_disea ...
written 7 months ago by
jcalis • 10
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... Dear all,
I wanted to ask if I can extend from the edgeR user manual 3.5 example, on between/within subjects comparisons.
I'm thinking on 3 ways I would like to extend:
1. Adding non-paired samples. From some patients I have only a single sample (ie not both tissueA and tissueB; for example, only ...
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... Thanks! I'll look into the models-approach and see how it compares with a limma-based analysis.
...
written 3.2 years ago by
jcalis • 10
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... Dear all,
I am trying to analyze a Stringtie based gene expression data set using ballgown, in a way similar to what was described for the analysis of difference of differences or interaction terms using voom+limma (see 9.5 in https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc ...
written 3.2 years ago by
jcalis • 10
• updated
3.2 years ago by
Alyssa Frazee • 210
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