User: thomas.wolfe

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Posts by thomas.wolfe

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Comment: C: topGO error using annFUN.org
... Worked for me too. Thx ...
written 23 months ago by thomas.wolfe0
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Comment: C: effect of polyploidy level on RUVs normalisation
... Thanks for your answer, I tried integrating the batch (as dates) in the EdgeR model. My problem mainly is that my "definition" of batch is arbitrary. I have some dates where there is only one sample preparation (in which case I use the year), some where there are two or more... As I do not really h ...
written 3.5 years ago by thomas.wolfe0
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Comment: C: effect of polyploidy level on RUVs normalisation
... Dear, Davide. Thank you for your answer, I answered on the post below too ...
written 3.6 years ago by thomas.wolfe0
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Answer: A: effect of polyploidy level on RUVs normalisation
... Dear Davide, thanks for the quick answer, I will try and elaborate the experimental design. we have  species (polyploidy) number of individual / nbr of technical replicates D. fuchsii (diploid) 4, 1 ind with tech rep D. incarnata (diploid) 5, 0 ind with tech rep ...
written 3.6 years ago by thomas.wolfe0
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effect of polyploidy level on RUVs normalisation
... Dear all, I am currently working with transcriptomic data obtained for diploid parental genomes and their polyploid progeny. When comparing polyploids to diploids for differential gene expression, what is the effect of polyploidy level on RUVs normalisation ? If anyone has a clear and possibly de ...
normalization ruvseq ruvs eda ruvnormalize written 3.6 years ago by thomas.wolfe0
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Technical Replicates and RUVs Normalisation
... Dear all, I am working with 19 RNAseq sample, 10 of which have 2 technical replicates (same individuals in a population). I am trying to correct for a clear batch effect using the RUVs approach as described in http://nar.oxfordjournals.org/content/early/2015/07/21/nar.gkv736.full and in the tutori ...

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