User: Raymond

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Raymond0
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Posts by Raymond

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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 24 days ago by Raymond0 • updated 24 days ago by Michael Love20k
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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 5 weeks 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 5 weeks ago by Raymond0 • updated 5 weeks ago by Michael Love20k
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Comment: C: Any difference between v$E and cpm(keep,log=TRUE)
... I'm much more clear now. Thanks Gordon. ...
written 6 weeks ago by Raymond0
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Any difference between v$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 7 weeks ago by Raymond0 • updated 7 weeks ago by Gordon Smyth35k
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Comment: C: PCA plot of variance stabilized transformation of normalized counts in limma
... Thanks, Gordon.  ...
written 7 weeks 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 7 weeks 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 7 weeks ago by Raymond0 • updated 7 weeks ago by Steve Lianoglou12k
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Comment: C: DESeq2 got stuck for one night, restarting?
... My design Matrix is design = ~ batch+genotype+sex+condition where batch has 9 level, genotype has 6 levels, sex has 2 levels, and condition has 4 levels. I do not include the PMI information here, where is a continuous number.  I will try limma-voom then. Thanks, Micheal! ...
written 9 weeks ago by Raymond0
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DESeq2 got stuck for one night, restarting?
... Hi,    My DESeq2 running was stucked for one night, it is normal?  My dataset contains 635 human samples, this is abnormally large: head(ddsTxi) class: DESeqDataSet dim: 6 635 metadata(1): version assays(2): counts avgTxLength dds <- DESeq(ddsTxi) estimating size factors   Note: levels of fac ...
rnaseq deseq2 written 9 weeks ago by Raymond0 • updated 9 weeks ago by Michael Love20k

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