Showing : PCa • reset
2
votes
3
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1.6k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 6 months ago by • 0
0
votes
0
replies
408
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
10 months ago feather-W • 0
0
votes
3
replies
1.1k
views
Biplot has a secondary x-axis and y-axis
pcaMethods pca
updated 11 months ago by 67k • written 11 months ago by • 0
8
votes
15
replies
2.5k
views
PCA percent variance DESeq2
PCA DESeq2
17 months ago IUH • 0
3
votes
12
replies
2.2k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
0
votes
3
replies
5.2k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 22 months ago by • 0 • written 22 months ago by • 0
0
votes
1
reply
638
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
votes
2
replies
1.2k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
1
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1
reply
1.4k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
4
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5
replies
2.9k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.8 years ago by • 0
2
votes
2
replies
1.7k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 2.9 years ago by 52k • written 2.9 years ago by ▴ 60
0
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0
replies
757
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
2.9 years ago Bruna • 0
5
votes
5
replies
2.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.9 years ago • updated 2.7 years ago 9906201a ▴ 20
0
votes
2
replies
2.0k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
1
vote
1
reply
1.1k
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
3.1 years ago Blobby123 • 0
0
votes
2
replies
2.0k
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
3.6 years ago Clara ▴ 10
4
votes
5
replies
1.7k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
1
vote
1
reply
951
views
Diffbind principal components
PCA DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
3
votes
15
replies
3.8k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 10
0
votes
1
reply
2.2k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 30
0
votes
10
replies
2.3k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
0
votes
0
replies
853
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
4.3 years ago Assa Yeroslaviz ★ 1.5k
2
votes
4
replies
8.7k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
2
votes
4
replies
2.0k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 3.1 years ago by ▴ 20 • written 4.4 years ago by ▴ 120
0
votes
1
reply
3.1k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
4.8 years ago cupret • 0
2
votes
6
replies
10.0k
views
Plot PCA with ellipses
pca
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 60
2
votes
1
reply
1.5k
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 30
1
vote
1
reply
1.0k
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
4
votes
5
replies
1.4k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
4.9 years ago svlachavas ▴ 840
1
vote
4
replies
1.8k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 80
2
votes
8
replies
3.9k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
0
votes
2
replies
1.2k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
1
vote
1
reply
1.2k
views
PCA axis description SNPRelate
SNPRelate PCA
updated 5.8 years ago by ▴ 890 • written 5.8 years ago by ▴ 60
1
vote
3
replies
1.2k
views
Deseq2 PCA Anlysis
deseq2 pca
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
3.0k
views
PCA analysis with 2 biological replicates
bayseq PCA
5.9 years ago bsad • 0
0
votes
3
replies
2.1k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 40
2
votes
1
reply
1.5k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
0
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0
replies
1.5k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.2 years ago kbobowik • 0
0
votes
7
replies
1.9k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
vote
4
replies
4.0k
views
Looking for Batch effects in PCA
batch effect pca
6.6 years ago • updated 2.0 years ago KB ▴ 50
2
votes
2
replies
1.5k
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
3
votes
6
replies
5.3k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 6.7 years ago by 67k • written 6.7 years ago by ▴ 120
1
vote
2
replies
2.1k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
6.8 years ago JoannaF ▴ 10
1
vote
3
replies
5.1k
views
PCA from TPM
pca tpm tximport
7.3 years ago tanyabioinfo ▴ 20
0
votes
5
replies
4.6k
views
PCA plot for TPM data
PCA
written 7.3 years ago by ▴ 20
12
votes
1
reply
8.0k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 80
9
votes
2
replies
2.0k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 7.3 years ago by ▴ 120 • written 7.3 years ago by ★ 7.9k
0
votes
6
replies
3.7k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
7.4 years ago • updated 7.3 years ago lirongrossmann ▴ 80
2
votes
3
replies
1.8k
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 7.4 years ago by ★ 5.2k • written 7.4 years ago by ▴ 20
0
votes
8
replies
7.5k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
7.5 years ago pkachroo ▴ 10
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
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