User: bio2001

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bio200160
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Posts by bio2001

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Answer: A: Confused in the usage of formula in DESeq or DESeq2
... Hi Michael, I need help in clarifying one aspect in these comparisons. I did run DESeq using a model similar to  what was discussed in this thread. ~ genotype + treatment + genotype:treatment I extract these results. 1. results(dds, name="genotypeM.treatmentT") 2. results(dds, contrast=c("tr ...
written 5 months ago by bio200160
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Using DESeq2: experimental design and extracting results
... Hi Michael, I'd like your suggestions on an additional question related to this previous thread on DESeq2. You might be aware that when publishing differential expression results, it is a convention to provide the mean and standard deviation values (after the normalization) for the genes being tes ...
visualization deseq deseq2 written 3.3 years ago by bio200160 • updated 3.3 years ago by Michael Love14k
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Comment: C: Using DESeq2: experimental design and extracting results
... Hi Michael, Thanks for explaining in detail. Just for clarification, I think we should add the "~" before the "genotype + time", right? Does "~" stand for formula notation in R? dds <- DESeq(dds, test="LRT", reduced=genotype + time) Also, when I do, dds <- nbinomWaldTest(dds, beta ...
written 3.4 years ago by bio200160
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Using DESeq2: experimental design and extracting results
... Hi, I have been a user of DESeq and recently DESeq2 for my research work. The latest DESeq2 seem to offer extensive differential testing options suitable for various experimental designs. Recently I wanted to use DESeq for a differential gene expression analysis between two plant genotypes across ...
deseq deseq2 written 3.4 years ago by bio200160 • updated 3.4 years ago by Michael Love14k

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