User: Simone

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Simone0
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Posts by Simone

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Comment: C: Limma: how to account for twin data (both MZ and DZ twins)?
... Re 3: I will split the data before voom, this seems indeed to be the better approach in this particular case. Re 4: With this, I will surely play around and try different options, with all samples and also comparing random subsamples of 9 to see how much the 'variability varies' within control sampl ...
written 26 days ago by Simone0
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Comment: C: Limma: how to account for twin data (both MZ and DZ twins)?
... I ran duplicateCorrelation on filtered and voom transformed counts. I did it for MZ, DZ, and I also created random pairs of singletons: > dupcor.mz$consensus [1] 0.5322475 > dupcor.dz$consensus [1] 0.3874335 > dupcor.rd$consensus [1] 0.1919584 This looks reasonable to me and is what I ...
written 27 days ago by Simone0
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Comment: C: DESeq2 design formula: how to account for twin data (MZ and DZ)?
... Thank you, Michael. I understand. However, would you be able to give a hint about where to find the section about modeling the different twin effects? When I search for the word "twin" in the DESeq2 vignette, I do not get any results, so I am not sure which section you refer to. I looked at the one ...
written 28 days ago by Simone0
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Limma: how to account for twin data (both MZ and DZ twins)?
... Hi again, I already posted my question, but was asked to open a new one because it was suggested to use limma instead of DESeq2: https://support.bioconductor.org/p/101991/#102058 A summary of the relevant parts of my question: I have to analyze some RNA-seq data, and I have got 400 samples of hum ...
limma design rna-seq formula twins written 28 days ago by Simone0 • updated 28 days ago by Aaron Lun17k
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Comment: A: DESeq2 design formula: how to account for twin data (MZ and DZ)?
... Hi Michael, Thank you very much for your reply. This is interesting, and I have got two more questions: 1) Regarding DESeq2 on MZ and DZ twins Out of curiosity, if there were no singletons in my data but only MZ and DZ twins, what would be the correct way of modelling it with DESeq2? Could I app ...
written 28 days ago by Simone0
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DESeq2 design formula: how to account for twin data (MZ and DZ)?
... Hi all, I have to analyze some RNA-seq data and I am using DESeq2 for this. However, the experimental design is somewhat complicated in this case and I am unsure about how to correctly define the design matrix for DESeq2. I am mostly following the “RNA-seq workflow: gene-level exploratory analysis ...
deseq2 design rna-seq formula twins written 29 days ago by Simone0

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