User: ricardo3889

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Posts by ricardo3889

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Normalized counts from DESeq2 results in similar but not equal total read count?
... Hi, I think this questioned has been asked before in different ways, but maybe someone can help mw understand this a bit better. My question stems from the need to visually represent the expression levels of a gene between my two groups. I know plotCounts() uses the normalized counts from counts(dds ...
normalization deseq2 written 6 months ago by ricardo38890 • updated 6 months ago by James W. MacDonald50k
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Comment: C: Log2FoldChange shrinkage method in DESeq2
... I also noticed a similar behavior of apeglm in my own RNAseq data set (10 samples), and I was wondering if in this case it is advised to use the "normal" method for shrinking the values instead of the newer apeglm. Any advise would be greatly appreciated. ...
written 6 months ago by ricardo38890
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Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... Is it possible to get these outputs you are referring to (FDR, FSR, posterior estimates of logFC) using DESeq2? I don't think the vignette explains this, unless I am missing something. I thought that FDR and the padj were used interchangeably. ...
written 6 months ago by ricardo38890
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Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... Thanks Kevin. I tried > EnhancedVolcano() + coord_cartesian(ylim=c(0,20)) And it works at setting the axis limits, but the data points outside of the visible plot are hidden. Is there a way to represent those values falling outside the visible plot with perhaps arrows, similar to the MA plots f ...
written 6 months ago by ricardo38890
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Comment: C: How to generate a volcano plot when p-values from DESeq2 are zero?
... Hi Kevin, thank you for your response. Yes I noticed this behavior, the problem is that volcano plot is zoomed out a lot to the point that it doesn't even look like a volcano anymore (see attached jpeg). is there a way to set the coordinate limits without dropping data observations (similar to coord ...
written 6 months ago by ricardo38890
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How to generate a volcano plot when p-values from DESeq2 are zero?
... When using DESeq2, I noticed that some of my top genes have a pvalue or padj of zero. I suppose the pvalue from the Wald test is really small and it got rounded at some point when I run DESeq2, although it is a bit surprising that other packages, including limma/voom, edgeR assigned a more reasonabl ...
rnaseq visualization deseq2 pvalue enhancedvolcano written 6 months ago by ricardo38890 • updated 6 months ago by Michael Love24k
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... Thank you Michael for your quick response! So as a bench researcher, I usually prioritize genes I want to study after a DE analysis based on adjusted P-values and FC. Would you say that the best way to do this is to use the adjP values from the analysis of the unnormalized counts from DESeq() and to ...
written 6 months ago by ricardo38890
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Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... When sorting DE genes by fold change, which method would you recommend to look at the top X genes with the highest logFC: a) the logFC from reslts(DESeq()) b) the logFC from rlog() and/or vst() c) the logFC from lfcShrink() Could someone please shed some light into this? maybe pros/cons of each ...
written 6 months ago by ricardo38890

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