HTML Code:
plotPCA(vsd, intgroup=c("conditions"))
12 results in 0.0030 seconds.
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How do I differentiate outliers from in-group variations in a DESeq2 PCA plot?
I have a PCA plot (please see below) from DESeq2'sfunction. I have 9 samples distributed in to... -
DESeq2 PCA Plots
Hello all,
I am running DESeq2 like so in R:
...Code:library(DESeq2) sTable = data.frame(sampleName = files, fileName = files,
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CummeRbund PCAplot RNA-sequencing
Hello all,
I'm using the PCAplot function in cummerbund and I was wondering if anyone knows how to display the variance explained for... -
PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw re
Which utility package (preferable web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or... -
pca
hello every one,
could you suggest me how to create 3d PCA plot with multivariate data as (need to plot PCA for samples not for genes)
... -
PCA plot in cummeRbund with subset genes
Hello all,
I'm trying to create a PCA plot with my data. I managed to create it with all my genes using the standard script:
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Interpreting a PCA plot produced with DESeq2
I've used DESeq2 to analyse a few RNA-Seq samples. I followed pretty closely the manual and using the following code
...Code:vsd <- varianceStabilizingTransformation(dds)
Last edited by feralBiologist; 02-14-2015, 05:30 PM. -
DESeq2 ntop set to 500?
Hi all,
I was just making some PCAs and I noticed that the plotPCA function within DESeq2 only takes the 500 genes with the highest variance.... -
Summarizing PCA in DESeq2
I am interested in knowing the proportion of variance that my components describe in the Principle Component Analysis in DESeq2. I have successfully been... -
cummeRbund PCA plot
Can anyone explain cummeRbund's PCA plot?
I do understand traditional PCA plots, like the one in DESeq, and cummeRbund's MDS plot, but what does... -
How to cluster samples with PCA in R?
Hi,
I have RNA-seq data for 16 mouse samples. I would like to cluster cufflinks results of these samples by PCA in R. The data looks like... -
meaning of DESeq PCA plot axis?
What does DESeq PCA plot axis mean?
If one sample has higher x- or y-value than others in the plot, does that mean it's better or worse...
