Showing : pca • reset
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
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
9
votes
2
replies
1.7k
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
9
votes
5
replies
5.7k
views
DESeq2 PCA different from Prcomp PCA
deseq2 Prcomp PCA
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 10
8
votes
15
replies
1.4k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago IUH • 0
6
votes
1
reply
14k
views
Deseq2 PCA plot customize
deseq2 pca
updated 8.3 years ago by 41k • written 8.3 years ago by ▴ 40
6
votes
4
replies
3.8k
views
How to generate a PCA scree plot in DESeq2?
pca deseq2 PCA scree plot
7.9 years ago CandiceChuDVM ▴ 40
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
2.2 years ago • updated 24 months ago 9906201a ▴ 20
5
votes
7
replies
3.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 2.7 years ago by ★ 5.2k • written 8.5 years ago by ▴ 20
4
votes
5
replies
2.8k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 7.5 years ago by ▴ 650 • written 7.5 years ago by ▴ 10
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
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
4
votes
5
replies
12k
views
How do I extract the principal components in DESeq2?
deseq2 pca
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 10
4
votes
2
replies
3.4k
views
PCA for voom normalized RNAseq data
voom pca
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 120
4
votes
5
replies
2.1k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 24 months ago by • 0
4
votes
1
reply
3.7k
views
PCA plot on DE genes do not separate samples. DESeq2.
deseq2 pca
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 10
4
votes
6
replies
1.4k
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by • 0
4
votes
5
replies
6.5k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
7.4 years ago wd ▴ 30
3
votes
2
replies
1.6k
views
How to find genes causing the high variance of one replicate in the PCA
pca variance deseq2 gene_id
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 10
3
votes
3
replies
1.6k
views
How to define an outlier array from PCA?
microarray PCA outliers sample outliers limma
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 60
3
votes
1
reply
2.0k
views
does pca assume no heteroscedasticity?
deseq2 pca
updated 8.2 years ago by 41k • written 8.2 years ago by ▴ 90
3
votes
15
replies
3.2k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by ▴ 10
3
votes
12
replies
1.5k
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
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
2
votes
6
replies
5.5k
views
PCA in DESeq2 - Can I get the genes contributing most to each component?
deseq2 pca
7.9 years ago Emily ▴ 10
2
votes
1
reply
2.1k
views
biplot diagram of PCA analysis differs from plot of variables
r pca biplot
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
2
votes
1
reply
3.3k
views
PCA from deseq and r function differ
deseq2 pca
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 80
2
votes
4
replies
8.9k
views
DESeq2 PCA plot: paired analysis
deseq2 pca
8.2 years ago g.atla ▴ 10
2
votes
16
replies
3.6k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
2
votes
2
replies
3.1k
views
DESeq2 transformation to use for PCA plot
deseq2 pca rlog transformation variancestabilizingtransformation
8.0 years ago Shobana Sekar ▴ 20
2
votes
2
replies
1.1k
views
Insert PCA in design model for adjusting
PCA
updated 7.5 years ago by 65k • written 7.5 years ago by ▴ 10
2
votes
1
reply
2.7k
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 7.5 years ago by 41k • written 7.5 years ago by ▴ 20
2
votes
2
replies
1.1k
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 10
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 ★ 5.2k • written 6.6 years ago by ▴ 20
2
votes
2
replies
1.3k
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
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
2
votes
8
replies
3.3k
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
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
2
votes
6
replies
7.1k
views
Plot PCA with ellipses
pca
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 60
2
votes
4
replies
1.5k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 2.4 years ago by ▴ 10 • written 3.7 years ago by ▴ 120
2
votes
4
replies
6.9k
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
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
1
vote
1
reply
782
views
Diffbind principal components
PCA DiffBind
updated 3.2 years ago by ★ 5.2k • written 3.2 years ago by • 0
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
1
vote
2
replies
979
views
nice 3D displays for PCA analysis
PCA
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 670
1
vote
1
reply
721
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by • 0
1
vote
2
replies
2.8k
views
DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq pca pasilla
updated 8.1 years ago by ▴ 150 • written 8.1 years ago by • 0
1
vote
1
reply
941
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 17 months ago by ★ 3.9k • written 17 months ago by • 0
1
vote
1
reply
857
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
2.4 years ago Blobby123 • 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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards • All
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Locations • All
France, 2 minutes ago
United States, 17 minutes ago
Belgium, 22 minutes ago
United Kingdom, 24 minutes ago
Ireland, 29 minutes ago
Traffic: 997 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6