User: Raymond

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Raymond0
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Posts by Raymond

<prev • 34 results • page 1 of 4 • next >
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Comment: C: ggplot2 category in category
... I figure out myself from kassambara's post: http://www.sthda.com/english/articles/32-r-graphics-essentials/132-plot-grouped-data-box-plot-bar-plot-and-more/ Thanks to kassambara, that post almost contain everything I wanted. Cheers, Raymond ...
written 3 months ago by Raymond0
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Comment: C: ggplot2 category in category
... I figure out myself from kassambara's post: http://www.sthda.com/english/articles/32-r-graphics-essentials/132-plot-grouped-data-box-plot-bar-plot-and-more/ Thanks to kassambara, that post almost contain everything I wanted. Cheers, Raymond ...
written 3 months ago by Raymond0
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(Closed) ggplot2 category in category
... Hi, My tmp4 contains the eigengene expression value, age ("young", "middle", "old"), and condition("control", "treatment"), and I want to have a boxplot, with all data point jittered within the box. I tried the following code, but the result is not what I wanted as the jitter plots are not separa ...
ggplot written 3 months ago by Raymond0
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Comment: C: DESeq2 GLM modelling and Wald's test
... Thanks for the comment. ...
written 4 months 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 4 months ago by Raymond0 • updated 4 months ago by Michael Love25k
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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 11 months ago by Raymond0 • updated 11 months ago by Michael Love25k
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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 11 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 11 months ago by Raymond0 • updated 11 months ago by Michael Love25k
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Comment: C: Any difference between v$E and cpm(keep,log=TRUE)
... I'm much more clear now. Thanks Gordon. ...
written 11 months ago by Raymond0
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Any difference between v$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 12 months ago by Raymond0 • updated 11 months ago by Gordon Smyth38k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Remove one sample from DESeq2 subject

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