User: Danie

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Danie40
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Posts by Danie

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Answer: A: How to design matrix on edgeR to study genotype x environmental interaction
... Dear Gordon, Thank you so much for your valuable input. I took sometime to study a bit more and be able to consider all the aspects you pointed out. At this time I reconsider the analysis and started again, with the data exploration of all 48 samples. First I filtered out the low reads, considerin ...
written 7.0 years ago by Danie40
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How to design matrix on edgeR to study genotype x environmental interaction
... Dear Gordon, Thank you so much for the reference. I read all the chapter regarding to the models and I tried to set up the following code considering a data frame like this: > target Sample Variety Location 1 1 CS Mont 2 2 CS Mont 3 25 CS Bol 4 ...
sequencing mirna edger written 7.0 years ago by Danie40
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How to design matrix on edgeR to study genotype x environmental interaction
... Dear all, I'm currently working with data coming from deep sequencing of 48 small RNAs libraries and using edgeR to identify DE miRNAs. I could not figure out how to design my matrix for the following experimental design: I have 2 varieties (genotypes), cultivated in 3 different locations (environ ...
sequencing edger written 7.0 years ago by Danie40
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Is normalization in edgeR required for small RNA sequencing data?
... Dear All, I am PhD student, currently working on differential expression analysis of my smallRNA library deep sequencing data and trying to identify differentially expressed miRNAs, using edgeR package. I have 24 different samples with 2 biological replicates (48 libraries). I am performing multip ...
sequencing smallrna edger written 7.1 years ago by Danie40 • updated 7.1 years ago by Mark Robinson870

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For Is normalization in edgeR required for small RNA sequencing data?

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