User: r.aprianto

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r.aprianto0
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Posts by r.aprianto

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Can DESeq2/edgeR perform differential analysis for rRNA?
... Hey Aaron, Thanks for the answer. What I forgot to mention is that I am working with bacterial transcriptome and it has 4 identical operons containing 23S, 16S and 5S rRNA. I am not sure I can make the first assumption. This holds true for some low variance genes but not necessarily for the entire ...
written 6 months ago by r.aprianto0
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Can DESeq2/edgeR perform differential analysis for rRNA?
... We obtained a non-rRNA-depleted libraries. Reads coming from the rRNA occupy 95% of all reads (ranging from 93-97%).  My question is simple: can we use/trust differential expression analysis (fold change, p-value) from DESeq2 or edgeR for these rRNAs? Especially since it is such very highly express ...
edger deseq2 differential gene expression rrna written 6 months ago by r.aprianto0
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Comment: C: Only one replicate: inferring dispersion from other group
... Dear Gordon, Thank you for the response. I wonder specifically for edgeR and limma-voom, whether there are any difference in how the package treat my dataset? Can you please specify where in the vignette this inference of variance is defined? Can individual gene dispersion and the inferred statist ...
written 3.6 years ago by r.aprianto0
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Comment: C: Only one replicate: inferring dispersion from other group
... Dear Simon, Thank you for the answer. Can you specify where in the DESeq2 vignette or other documentation this (very useful) behavior is defined? Is there any degree of confidence of this estimation? If I have two strains (A1 (2 replicates), A2 (2 replicates), B1 (2), B2 (2), C1 (2), C2 (2), D1 (1 ...
written 3.6 years ago by r.aprianto0
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Comment: C: Only one replicate: inferring dispersion from other group
... Sorry if the question was unclear. I have four groups as mentioned above and I want to use the 4th group which only contains 1 replicate as opposed to 2 replicates for the other groups. Differential expression is then performed between those groups. ...
written 3.6 years ago by r.aprianto0
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Only one replicate: inferring dispersion from other group
... Dear all, I have a general question regarding RNA-Seq analysis to identify Differentially Expressed Genes (DEGs). Basically I want to do statistical analysis from one replicate. I have the following design: Group A (time point 1)      2 replicates Group B (time point 2)      2 replicates Grou ...
limma edger deseq2 differential gene expression written 3.6 years ago by r.aprianto0 • updated 3.6 years ago by Gordon Smyth34k

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For Only one replicate: inferring dispersion from other group

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