Showing : PCa • reset
0
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91
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
19 days ago feather-W • 0
0
votes
3
replies
313
views
Biplot has a secondary x-axis and y-axis
pcaMethods pca
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
8
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15
replies
1.4k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago • updated 7 months ago IUH • 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
0
votes
3
replies
2.9k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 12 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
416
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
votes
2
replies
824
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 13 months ago by ★ 1.3k • written 13 months ago by • 0
1
vote
1
reply
930
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 17 months ago by ★ 3.9k • written 17 months ago by • 0
4
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5
replies
2.0k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 24 months ago by • 0
2
votes
2
replies
1.2k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 60
0
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0
replies
559
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
2.1 years ago Bruna • 0
5
votes
5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.1 years ago • updated 23 months ago 9906201a ▴ 20
0
votes
2
replies
1.5k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by • 0
1
vote
1
reply
848
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
2.4 years ago Blobby123 • 0
0
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2
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1.7k
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
2.8 years ago Clara • 0
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
1
reply
774
views
Diffbind principal components
PCA DiffBind
updated 3.2 years ago by ★ 5.1k • written 3.2 years ago by • 0
3
votes
15
replies
3.1k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by ▴ 20
0
votes
10
replies
1.7k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 10
0
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0
replies
664
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
3.5 years ago Assa Yeroslaviz ★ 1.5k
2
votes
4
replies
6.8k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 3.6 years ago by 50k • written 3.6 years ago by • 0
2
votes
4
replies
1.5k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 2.3 years ago by ▴ 10 • written 3.7 years ago by ▴ 120
0
votes
1
reply
2.3k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
4.0 years ago cupret • 0
2
votes
6
replies
7.0k
views
Plot PCA with ellipses
pca
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 60
2
votes
1
reply
1.1k
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by ▴ 20
1
vote
1
reply
709
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 4.1 years ago by ★ 5.1k • written 4.1 years ago by • 0
4
votes
5
replies
1.1k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
4.2 years ago svlachavas ▴ 830
1
vote
4
replies
1.4k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 80
2
votes
8
replies
3.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 10
0
votes
2
replies
884
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
1
vote
1
reply
961
views
PCA axis description SNPRelate
SNPRelate PCA
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by ▴ 60
1
vote
3
replies
991
views
Deseq2 PCA Anlysis
deseq2 pca
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
1
reply
2.4k
views
PCA analysis with 2 biological replicates
bayseq PCA
5.1 years ago bsad • 0
0
votes
3
replies
1.8k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 40
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
0
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0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.4 years ago kbobowik • 0
0
votes
7
replies
1.5k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
1
vote
4
replies
3.4k
views
Looking for Batch effects in PCA
batch effect pca
5.8 years ago • updated 15 months ago KB ▴ 50
2
votes
2
replies
1.2k
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 10
3
votes
6
replies
4.8k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 110
1
vote
2
replies
1.7k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
6.0 years ago JoannaF ▴ 10
1
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3
replies
4.4k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
0
votes
5
replies
3.7k
views
PCA plot for TPM data
PCA
written 6.5 years ago by ▴ 20
12
votes
1
reply
7.1k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
9
votes
2
replies
1.6k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 6.5 years ago by ▴ 110 • written 6.5 years ago by ★ 7.9k
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.6 years ago lirongrossmann ▴ 80
2
votes
3
replies
1.5k
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 6.6 years ago by ★ 5.1k • written 6.6 years ago by ▴ 20
0
votes
8
replies
6.6k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
6.7 years ago pkachroo ▴ 10
9
votes
7
replies
11k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 6.8 years ago by ▴ 10 • written 6.8 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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