Showing : pca • reset
8
votes
15
replies
868
views
PCA percent variance DESeq2
PCA DESeq2
3 months ago IUH • 0
3
votes
12
replies
1.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 7 months ago by 41k • written 7 months ago by ▴ 10
0
votes
3
replies
1.7k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 8 months ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
314
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 8 months ago by ▴ 740 • written 8 months ago by • 0
0
votes
2
replies
551
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
1
vote
1
reply
726
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 12 months ago by 3.9k • written 12 months ago by • 0
4
votes
5
replies
1.7k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 19 months ago by • 0
2
votes
2
replies
998
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 20 months ago by 49k • written 20 months ago by ▴ 60
0
votes
0
replies
465
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
21 months ago Bruna • 0
5
votes
5
replies
1.4k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
21 months ago • updated 19 months ago 9906201a ▴ 20
0
votes
2
replies
1.3k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
1
vote
1
reply
726
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
24 months ago Blobby123 • 0
0
votes
2
replies
1.5k
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
2.5 years ago Clara • 0
4
votes
5
replies
1.2k
views
DEseq2 results
heatmaps DEGs PCA
updated 2.8 years ago by 3.9k • written 2.8 years ago by • 0
1
vote
1
reply
673
views
Diffbind principal components
PCA DiffBind
updated 2.8 years ago by ★ 5.1k • written 2.8 years ago by • 0
3
votes
15
replies
2.8k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.0 years ago by 3.9k • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 3.0 years ago by 3.9k • written 3.0 years ago by ▴ 20
0
votes
10
replies
1.5k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 3.1 years ago by 41k • written 3.1 years ago by ▴ 10
0
votes
0
replies
571
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
3.2 years ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
5.8k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 3.2 years ago by 49k • written 3.2 years ago by • 0
2
votes
4
replies
1.3k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 24 months ago by ▴ 10 • written 3.3 years ago by ▴ 120
0
votes
1
reply
1.8k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
3.6 years ago cupret • 0
2
votes
6
replies
6.1k
views
Plot PCA with ellipses
pca
updated 3.6 years ago by 41k • written 3.6 years ago by ▴ 50
2
votes
1
reply
894
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 3.7 years ago by 3.9k • written 3.7 years ago by ▴ 20
1
vote
1
reply
578
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 3.7 years ago by ★ 5.1k • written 3.7 years ago by • 0
4
votes
5
replies
902
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
3.8 years ago svlachavas ▴ 820
1
vote
4
replies
1.2k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 80
2
votes
8
replies
2.8k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 4.5 years ago by 41k • written 4.5 years ago by ▴ 10
0
votes
2
replies
764
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 10
1
vote
1
reply
862
views
PCA axis description SNPRelate
SNPRelate PCA
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by ▴ 60
1
vote
3
replies
888
views
Deseq2 PCA Anlysis
deseq2 pca
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
1
reply
2.2k
views
PCA analysis with 2 biological replicates
bayseq PCA
4.7 years ago bsad • 0
0
votes
3
replies
1.6k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
2
votes
1
reply
1.1k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
0
votes
0
replies
1.1k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.0 years ago kbobowik • 0
0
votes
7
replies
1.4k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
1
vote
4
replies
3.2k
views
Looking for Batch effects in PCA
batch effect pca
5.4 years ago • updated 10 months ago KB ▴ 50
2
votes
2
replies
1.1k
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 10
3
votes
6
replies
4.6k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 5.6 years ago by 64k • written 5.6 years ago by ▴ 110
1
vote
2
replies
1.6k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
5.6 years ago JoannaF ▴ 10
1
vote
3
replies
4.1k
views
PCA from TPM
pca tpm tximport
6.1 years ago tanyabioinfo ▴ 20
0
votes
5
replies
3.3k
views
PCA plot for TPM data
PCA
written 6.1 years ago by ▴ 20
12
votes
1
reply
6.7k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 80
9
votes
2
replies
1.5k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 6.1 years ago by ▴ 110 • written 6.1 years ago by 7.8k
0
votes
6
replies
2.8k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.2 years ago lirongrossmann ▴ 80
2
votes
3
replies
1.4k
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 6.2 years ago by ★ 5.1k • written 6.2 years ago by ▴ 20
0
votes
8
replies
6.1k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
6.4 years ago pkachroo ▴ 10
9
votes
7
replies
10k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 6.4 years ago by ▴ 10 • written 6.4 years ago by ▴ 30
0
votes
1
reply
988
views
pca plot for tissues and protein values
pca
updated 6.5 years ago by 64k • written 6.5 years ago by ▴ 40
0
votes
0
replies
1.0k
views
gage pca loadings
pca gage loadings
6.7 years ago MT ▴ 10
50 results • Page 1 of 1
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Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change by James W. MacDonald 64k
You could look at my answer and extrapolate from there.
Comment: enrichGOgradient color change by WU • 0
I would like to ask how to make the counts legend black. Thank you.
Answer: Problems with FLOWAI by Alexander • 0
Hi. The length of the file path, or whether the files are local on the computer has nothing to do with it in my experience. I watched the a…
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Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
How to know if I should use voomWithQualityWeights() or not?
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