User: Raymond

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Raymond0
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Posts by Raymond

<prev • 31 results • page 1 of 4 • next >
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Comment: C: DESeq2 GLM modelling and Wald's test
... Thanks for the comment. ...
written 12 days ago by Raymond0
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Too many DEGs
... Hi, I have 36 animals and got two tissues of each animal for RNAseq. My design model is: sample+tissue and I got DEG results like that: out of 16445 with nonzero total read count adjusted p-value < 0.05 LFC > 0 (up) : 7276, 44% LFC < 0 (down) : 7508, 46% outliers [1] ...
deseq2 written 12 days ago by Raymond0 • updated 11 days ago by Michael Love24k
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How to decide whether a variate should be in the model or not
... Hi, all/Micheal Love,   Is there a way in DESeq2 package to hep with this kind of problems? For example, I may be able to think of tens of possible variables that may affect gene expressions(Genotypes of a couple of genes, genders, age, PMI, RIN, RIN^2, mapping rate, batches....). Obviously, I shou ...
rnaseq deseq2 written 7 months ago by Raymond0 • updated 7 months ago by Michael Love24k
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Comment: C: Any way to get a p-value for multiple comparisons in DESeq2?
... This is exactly what I want! Thanks, Michael! ...
written 8 months ago by Raymond0
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Any way to get a p-value for multiple comparisons in DESeq2?
... Hi,    I had samples with three groups,"Control","TreatA","TreatB". For each gene, I used DESeq2 contrast to get the p-values of "TreatA vs Control" , "TreatB vs Control" and "TreatA vs TreatB".    Now I want to test the hypothesis that: The expression of Gene X is not changed in any of these thr ...
deseq2 written 8 months ago by Raymond0 • updated 8 months ago by Michael Love24k
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Comment: C: Any difference between v$E and cpm(keep,log=TRUE)
... I'm much more clear now. Thanks Gordon. ...
written 8 months ago by Raymond0
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Any difference between v$E and cpm(keep,log=TRUE)
... Hi,   I got the following code, and want to generate the heatmap later.  y <- calcNormFactors(y, method = "TMM") v <- voom(y, design, plot=TRUE)   lcpm <- cpm(y, log=TRUE) From EdgeR, it was recommended that lcpm could be used to generate heatmap with a prior.count. However, from http ...
limma written 8 months ago by Raymond0 • updated 8 months ago by Gordon Smyth37k
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Comment: C: PCA plot of variance stabilized transformation of normalized counts in limma
... Thanks, Gordon.  ...
written 8 months ago by Raymond0
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Comment: C: PCA plot of variance stabilized transformation of normalized counts in limma
... Thanks, Gordon. Based on your experience, when would you set 'gene.selection="common" ', and when ' gene.selection="pairwise" '? Is there any rule of thumb?  ...
written 8 months ago by Raymond0
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PCA plot of variance stabilized transformation of normalized counts in limma
... Hi,     I used to plot PCA  using DESeq2, and it works great.  In DESeq2, the normalized counts are transformed through vst(variance stabilized transformation, based on the NB variance ~ expectation relationships?) function, rather than the direct log transformed counts.     I tried limma-voom in ...
edger deseq2 limma-voom written 8 months ago by Raymond0 • updated 8 months ago by Steve Lianoglou12k

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