User: aec

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aec40
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Posts by aec

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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... thanks Michael.  ...
written 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks 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 12 weeks 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 12 weeks ago by aec40 • updated 12 weeks ago by Michael Love18k
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Comment: C: weird behaviour DESeq2 1.18.1
... Thanks a lot for the appropriate reply Michael. ...
written 4 months ago by aec40
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Comment: C: weird behaviour DESeq2 1.18.1
... Michael, these are normalized counts (scale="row"). What happens here is that I have three different groups and I have to perform pairwise comparisons and I run the DESEq2 just once and extract the desired comparisons. Your filter only works if I run DESeq2 every time for the desired comparison. Eac ...
written 4 months ago by aec40
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Comment: C: weird behaviour DESeq2 1.18.1
... Michael, it is what I did and the filtering did not solve the problem ( I have explained it above). ...
written 4 months ago by aec40
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weird behaviour DESeq2 1.18.1
... Dear all, Since I am using DESeq2 version 1.18.1 I observe a weird behaviour with the significant genes. As you can see on the heatmap below, the top 50 most significant genes are plotted (FDR<5%) and it is full of outliers. I am running DESeq2 with default options. I also tried to pre-filter th ...
deseq2 outliers version written 4 months ago by aec40 • updated 4 months ago by Michael Love18k

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