Showing : pca • reset
1
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134
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PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 12 weeks ago by 3.7k • written 12 weeks ago by • 0
3
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5
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670
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DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 9 months ago by • 0
2
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2
replies
483
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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
0
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0
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227
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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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737
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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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711
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 13 months ago by ★ 1.2k • written 13 months ago by • 0
1
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1
reply
432
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
14 months ago Blobby123 • 0
0
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2
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789
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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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732
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DEseq2 results
heatmaps DEGs PCA
updated 23 months ago by 3.7k • written 23 months ago by • 0
1
vote
1
reply
432
views
Diffbind principal components
PCA DiffBind
updated 24 months ago by ★ 4.6k • written 24 months ago by • 0
3
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15
replies
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
0
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1
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870
views
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
0
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10
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1.0k
views
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
0
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0
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358
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contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
2.3 years ago Assa Yeroslaviz ★ 1.5k
1
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4
replies
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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899
views
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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926
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
2.8 years ago cupret • 0
2
votes
6
replies
4.2k
views
Plot PCA with ellipses
pca
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 40
0
votes
1
reply
474
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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327
views
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
replies
556
views
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
replies
707
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
replies
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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533
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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
vote
1
reply
600
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
replies
594
views
Deseq2 PCA Anlysis
deseq2 pca
updated 3.9 years ago by 39k • written 3.9 years ago by • 0
0
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1
reply
1.6k
views
PCA analysis with 2 biological replicates
bayseq PCA
3.9 years ago bsad • 0
0
votes
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
votes
1
reply
852
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
0
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0
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748
views
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
replies
2.4k
views
Looking for Batch effects in PCA
batch effect pca
4.6 years ago • updated 20 days ago KB ▴ 50
2
votes
2
replies
751
views
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
3
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6
replies
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
1
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2
replies
1.3k
views
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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3.2k
views
PCA from TPM
pca tpm tximport
5.3 years ago tanyabioinfo ▴ 20
0
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3
replies
2.4k
views
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
reply
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
votes
2
replies
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
0
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6
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2.0k
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
views
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
votes
8
replies
4.8k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
5.5 years ago pkachroo ▴ 10
9
votes
7
replies
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
reply
739
views
pca plot for tissues and protein values
pca
updated 5.7 years ago by 62k • written 5.7 years ago by ▴ 40
0
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0
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837
views
gage pca loadings
pca gage loadings
5.9 years ago MT ▴ 10
2
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2
replies
886
views
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
votes
5
replies
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
replies
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
votes
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 6.3 years ago by 39k • written 6.3 years ago by ▴ 20
4
votes
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: DESeq2 and heatmap for multiple comparisons by artem.vorobyev • 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets by nicklesteele532 • 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions? by Hervé Pagès 16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons by swbarnes2 ★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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