User: BharathAnanth

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Posts by BharathAnanth

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Comment: C: limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
... Hi Aaron Thank you for an in depth answer (as usual). On 4) What might the flaws be if had only one group of 10 samples (i.e., no blocks within my data) and I performed the library label shuffling? I am trying to understand the problems in this particular context a bit better.  Thanks. ...
written 11 months ago by BharathAnanth70
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limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
...   Hi I have the following experimental set up. I have RNA-seq time series data that span (0h,2h,....22h) and am interested in temporal patterns of  gene regulation. However, the data was constructed by sampling repeatedly two cultures that are (in time) 11h apart. In other words, samples 0,2,..10 ...
duplicatecorrelation limma voom voomwithqualityweights written 11 months ago by BharathAnanth70 • updated 11 months ago by Aaron Lun24k
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Comment: C: cameraPR vs geneSetTest and ROAST/CAMERA in general
... Hi Aaron Thank you for your reply. If I may ask a couple of follow up questions. 1. Suppose I have identified a set of genes from analysis of one data set and want to test if these same genes are interestingly regulated in another dataset. Could I still use camera()/geneSetTest() (to compare again ...
written 14 months ago by BharathAnanth70
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cameraPR vs geneSetTest and ROAST/CAMERA in general
...   Hi!   I learnt from the this old post (https://support.bioconductor.org/p/60382/) that ROAST cannot be performed on multiple contrasts (i.e., with the F-test). This is still true, I suppose? In that post it was suggested to use geneSetTest with Fstatistic (from topTable). First, my understanding ...
limma gene set analysis voomwithqualityweights written 14 months ago by BharathAnanth70 • updated 14 months ago by Aaron Lun24k
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Comment: C: glmTreat Errors for multi coefficient and analysis of deviance situations.
... Normally the null hypothesis for the glm would be (in my case) H0: c=0 AND s =0. What I want to test is the null hypothesis H0: |c| < lfc AND |s| <lfc using glmTreat. Is this inconceivable?   ...
written 18 months ago by BharathAnanth70
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glmTreat Errors for multi coefficient and analysis of deviance situations.
... Hi   I am fitting some time course RNA-seq data using glmQLFit and I then wanted to use glmTreat to test either of two coefficients with 0.5 lfc. Here is the simplified version (with fewer samples). set.seed(0) T <- 24 t <- rep(seq(3,42, by=3), 11) c <- cos(2*pi*t/T) # a time course bas ...
edger glmtreat analysis of deviance written 18 months ago by BharathAnanth70 • updated 18 months ago by Ryan C. Thompson7.3k
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Comment: C: edgeR: multi-subject time series analysis
... Thanks Aaron for your clarifications.  A further question. In design1, are we testing that the average time behavior is the same or that time behavior is the same for all subjects? I guess that is a subtle difference. The former would permit genes that have the same behavior in say 6 out of 11 subj ...
written 18 months ago by BharathAnanth70
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Comment: C: edgeR: multi-subject time series analysis
...   Sorry, I didnt realize you want a piece of code you could just run. Here goes .... T <- 24 t <- rep(seq(3,42, by=3), 11) c <- cos(2*pi*t/T) # a time course basis function s <- sin(2*pi*t/T) batch_effect <- factor(ceiling(runif(14*11)*11)) subjects <- sprintf("P%02d", ...
written 18 months ago by BharathAnanth70
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Comment: C: edgeR: multi-subject time series analysis
... t <- seq(0,42, by=3) c <- cos(2*pi*t/T) # a time course basis function s <- sin(2*pi*t/T) batch_effect <- (e.g., subjects (1,4,10), (2,5,11), (3,6,9), (7,8) were sequenced together ) # sequencing libraries subjects <- rep(1:11, each = 14) Initially I only, used design1 <- ...
written 18 months ago by BharathAnanth70
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edgeR: multi-subject time series analysis
... Hi   I have a time series RNA-seq data from multiple subjects -- 14 time points each for 11 subjects. I am interested in finding inter-individual differences in expression and genes with similar expression across subjects. I looked at the example 3.5 in the EdgeR User Manual. I fit using the QL fra ...
timecourse edger multiple groups written 18 months ago by BharathAnanth70 • updated 18 months ago by Aaron Lun24k

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