User: aec

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aec40
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Posts by aec

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Comment: C: time series, block by patient, between and within comparisons limma-voom
... Yes, irrespective of the group. ...
written 5 days ago by aec40
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... I have 5 time points per patient, in total 15 patients. These 15 patients can be further divided in two groups for question b) ...
written 6 days ago by aec40
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... sure, I will edit my post. ...
written 6 days ago by aec40
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time series, block by patient, between and within comparisons limma-voom
... Dear all, I have a time course RNA-seq analysis with the following design: 5 time points, 15 patients, 2 types of patients. the questions I would like to answer: a) expression differences across time points irrespective of patient type (t1 vs t2, t1 vs t3, ...) b) expression differences between ...
rna-seq patient limma-voom time series written 7 days ago by aec40 • updated 3 days ago by Aaron Lun21k
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... thanks Michael.  ...
written 4 months ago by aec40
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... n.sv <- num.sv(dat,mod) n.sv [1] 1   ...
written 4 months ago by aec40
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... dds <- estimateSizeFactors(dds) dat <- counts(dds, normalized=TRUE) idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod <- model.matrix(~case, colData(dds)) mod0 <- model.matrix(~1, colData(dds)) n.sv <- num.sv(dat,mod,method="leek") n.sv [1] 589   ...
written 4 months ago by aec40
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differential expression analysis with big dataset and >500 surrogate variables
... dear all, I have more than 500 RNA-seq samples and have to compare cases vs controls. I first run SVA to remove unknown variation and found >500 surrogate variables. Is a good practice to perform a LRT test with deseq2 where full model =~case+SV1+SV2+SVn and reduced model=~case to know how many ...
sva deseq2 differential expression lrt written 4 months ago by aec40
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Comment: C: interaction model deseq2 specific DE genes
... ok Michael, so none of this contrasts answer my question directly right? res = results(dds, contrast=c("temp","temp24",temp"21")) res = results(dds, name="strain2.temp24") res = results(dds, name="strain3.temp24") res = results(dds, contrast=list("strain3.temp24", "strain2.temp24")) ...
written 4 months ago by aec40
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interaction model deseq2 specific DE genes
... Dear all, I have a design with temperature (2-levels: 21º C and 24º C) and strain (3-levels: strain1, strain2, strain3) and I would like to find differentially expressed genes specific to each strain for the 24º C vs 21º C comparison. That means: 1) finding those genes that are differentially expr ...
deseq2 differential expression interaction model written 5 months ago by aec40 • updated 5 months ago by Michael Love19k

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Popular Question 15 months ago, created a question with more than 1,000 views. For limma - complex design with paired samples, sex and batch effect

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