User: jcalis

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jcalis • 10
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Posts by jcalis

<prev • 6 results • page 1 of 1 • next >
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Comment: C: EdgeR between/within comparisons (3.5) with nested non-balanced data set
... 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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Comment: C: EdgeR between/within comparisons (3.5) with nested non-balanced data set
... 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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Comment: C: EdgeR between/within comparisons (3.5) with nested non-balanced data set
... 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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EdgeR between/within comparisons (3.5) with nested non-balanced data set
... 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 ...
edger glm nested glmqlfit written 7 months ago by jcalis • 10 • updated 7 months ago by Aaron Lun • 25k
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Comment: C: Interaction term analysis using ballgown
... 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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Interaction term analysis using ballgown
... 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 ...
rnaseq differential gene expression ballgown stringtie voom limma written 3.2 years ago by jcalis • 10 • updated 3.2 years ago by Alyssa Frazee • 210

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