Showing : PCA • reset
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130
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PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 11 weeks ago by 3.7k • written 11 weeks ago by • 0
3
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5
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659
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DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 9 months ago by • 0
2
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2
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478
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Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 10 months ago by 47k • written 10 months ago by ▴ 60
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0
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224
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LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
11 months ago Bruna • 0
5
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5
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727
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First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
11 months ago • updated 9 months ago 9906201a ▴ 20
0
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2
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701
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 12 months ago by ★ 1.2k • written 12 months ago by • 0
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1
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428
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mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
14 months ago Blobby123 • 0
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2
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780
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
20 months ago Clara • 0
4
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5
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728
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DEseq2 results
heatmaps DEGs PCA
updated 23 months ago by 3.7k • written 23 months ago by • 0
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1
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432
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Diffbind principal components
PCA DiffBind
updated 24 months ago by ★ 4.6k • written 24 months ago by • 0
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15
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1.9k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 2.1 years ago by 3.7k • written 2.1 years ago by ▴ 10
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1
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860
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Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 2.2 years ago by 3.7k • written 2.2 years ago by • 0
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10
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1.0k
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Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 2.3 years ago by 39k • written 2.3 years ago by ▴ 10
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357
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contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
2.3 years ago Assa Yeroslaviz ★ 1.5k
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4
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3.6k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 2.4 years ago by 47k • written 2.4 years ago by • 0
2
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4
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893
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Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 13 months ago by ▴ 10 • written 2.5 years ago by ▴ 120
0
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1
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921
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Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
2.8 years ago cupret • 0
2
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6
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4.2k
views
Plot PCA with ellipses
pca
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 40
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1
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473
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 2.9 years ago by 3.7k • written 2.9 years ago by • 0
1
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1
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325
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DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 2.9 years ago by ★ 4.6k • written 2.9 years ago by • 0
4
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5
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550
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Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
3.0 years ago svlachavas ▴ 800
1
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4
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704
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 3.3 years ago by 39k • written 3.3 years ago by ▴ 50
2
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8
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1.9k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 3.7 years ago by 39k • written 3.7 years ago by ▴ 10
0
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2
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530
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diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 10
1
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1
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598
views
PCA axis description SNPRelate
SNPRelate PCA
updated 3.9 years ago by ▴ 840 • written 3.9 years ago by ▴ 60
1
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3
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594
views
Deseq2 PCA Anlysis
deseq2 pca
updated 3.9 years ago by 39k • written 3.9 years ago by • 0
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1
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1.6k
views
PCA analysis with 2 biological replicates
bayseq PCA
3.9 years ago bsad • 0
0
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3
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1.1k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 4.1 years ago by 39k • written 4.1 years ago by ▴ 40
2
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1
reply
851
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
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0
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747
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
4.2 years ago kbobowik • 0
0
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7
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1.1k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 4.4 years ago by 39k • written 4.4 years ago by • 0
1
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4
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2.4k
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Looking for Batch effects in PCA
batch effect pca
4.6 years ago • updated 18 days ago KB ▴ 50
2
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2
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749
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DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 4.7 years ago by 39k • written 4.7 years ago by ▴ 10
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6
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4.0k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 4.8 years ago by 62k • written 4.8 years ago by ▴ 110
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2
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1.3k
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DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
4.8 years ago JoannaF ▴ 10
1
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3
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3.1k
views
PCA from TPM
pca tpm tximport
5.3 years ago tanyabioinfo ▴ 20
0
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3
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2.4k
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PCA plot for TPM data
PCA
updated 5.3 years ago by ▴ 60 • written 5.3 years ago by ▴ 20
12
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1
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5.7k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 5.3 years ago by 39k • written 5.3 years ago by ▴ 70
9
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2
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1.1k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 5.3 years ago by ▴ 110 • written 5.3 years ago by 7.8k
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6
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1.9k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
5.4 years ago lirongrossmann ▴ 70
2
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3
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1.1k
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Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 5.4 years ago by ★ 4.6k • written 5.4 years ago by ▴ 20
0
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8
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4.8k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
5.5 years ago pkachroo ▴ 10
9
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7
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9.3k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 5.6 years ago by ▴ 10 • written 5.6 years ago by ▴ 30
0
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1
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737
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pca plot for tissues and protein values
pca
updated 5.7 years ago by 62k • written 5.7 years ago by ▴ 40
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0
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836
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gage pca loadings
pca gage loadings
5.8 years ago MT ▴ 10
2
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2
replies
884
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pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 5.9 years ago by 62k • written 5.9 years ago by ▴ 10
4
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5
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5.3k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
6.2 years ago wd ▴ 30
1
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2
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1.1k
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 6.2 years ago by ▴ 150 • written 6.2 years ago by • 0
2
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1
reply
1.9k
views
how to plot PCA for only one of two groups compared or plot three groups at a time
deseq2 bioconductor rna-seq pca
updated 6.2 years ago by 39k • written 6.3 years ago by ▴ 20
4
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5
replies
2.1k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 6.3 years ago by ▴ 640 • written 6.3 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: TCGA: clinical data and expression data by sharifnstu1203002m • 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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