Hello,
I have 16 samples from 16 different human tissues (say "A","B",...,"P"), so no biological replicates (75bp single end reads). I want to study the expression levels of a specific group of genes for a specific tissue (let's say this tissue is "B"). A few questions on this scenario:
1. Is it valid to treat tissue B as 1 condition and the other 15 tissues as replicates for the "non-B" condition?
2. Although I'm only interested in a specific group of genes, is it recommended to supply DESeq with a count table of all genes instead of only the few genes, I'm interested in? (in order to give DESeq more information about the samples)
3. If 1. is ok: Is the following configuration a good choice for the dispersion estimation?
4. What would be the explanatory power of the analysis? (My hope is that 16 different samples give enough information to obtain meaningful results, despite the absence of replicates?!)
5. Would it be a great improvement to use technical replicates? (either 50bp paired end or 100bp stranded)
Thank you.
edit: added point 5
I have 16 samples from 16 different human tissues (say "A","B",...,"P"), so no biological replicates (75bp single end reads). I want to study the expression levels of a specific group of genes for a specific tissue (let's say this tissue is "B"). A few questions on this scenario:
1. Is it valid to treat tissue B as 1 condition and the other 15 tissues as replicates for the "non-B" condition?
2. Although I'm only interested in a specific group of genes, is it recommended to supply DESeq with a count table of all genes instead of only the few genes, I'm interested in? (in order to give DESeq more information about the samples)
3. If 1. is ok: Is the following configuration a good choice for the dispersion estimation?
Code:
estimateDispersions(cds,method="blind",sharingMode="fit-only",fitType="local")
5. Would it be a great improvement to use technical replicates? (either 50bp paired end or 100bp stranded)
Thank you.
edit: added point 5
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