Showing : PCA • reset
4
votes
5
replies
177
views
DEseq2 results
heatmaps DEGs PCA
updated 9 weeks ago by 2.9k • written 9 weeks ago by • 0
1
vote
1
reply
92
views
Diffbind principal components
PCA DiffBind
updated 11 weeks ago by ★ 3.8k • written 11 weeks ago by • 0
3
votes
15
replies
471
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 4 months ago by 2.9k • written 4 months ago by ▴ 10
0
votes
1
reply
135
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 5 months ago by 2.9k • written 5 months ago by • 0
0
votes
10
replies
307
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 6 months ago by 32k • written 6 months ago by ▴ 10
0
votes
0
replies
80
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
6 months ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
202
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 8 months ago by 42k • written 8 months ago by • 0
2
votes
3
replies
211
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 8 months ago by 2.9k • written 8 months ago by ▴ 100
0
votes
1
reply
86
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
12 months ago cupret • 0
2
votes
6
replies
732
views
Plot PCA with ellipses
pca
updated 12 months ago by 32k • written 12 months ago by ▴ 40
0
votes
1
reply
75
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 13 months ago by 2.9k • written 13 months ago by • 0
1
vote
1
reply
69
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 13 months ago by ★ 3.8k • written 13 months ago by • 0
4
votes
5
replies
165
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
14 months ago svlachavas ▴ 780
1
vote
4
replies
239
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 19 months ago by 32k • written 19 months ago by ▴ 50
1
vote
8
replies
649
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 23 months ago by 32k • written 23 months ago by • 0
0
votes
2
replies
244
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.1 years ago by ★ 26k • written 2.1 years ago by ▴ 10
1
vote
1
reply
223
views
PCA axis description SNPRelate
SNPRelate PCA
updated 2.1 years ago by ▴ 800 • written 2.1 years ago by ▴ 60
1
vote
3
replies
281
views
Deseq2 PCA Anlysis
deseq2 pca
updated 2.1 years ago by 32k • written 2.1 years ago by • 0
0
votes
1
reply
543
views
PCA analysis with 2 biological replicates
bayseq PCA
2.1 years ago bsad • 0
0
votes
3
replies
422
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 2.3 years ago by 32k • written 2.3 years ago by ▴ 40
2
votes
1
reply
420
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 2.4 years ago by ★ 26k • written 2.4 years ago by • 0
0
votes
0
replies
339
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
2.5 years ago kbobowik • 0
0
votes
7
replies
583
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 2.7 years ago by 32k • written 2.7 years ago by • 0
0
votes
3
replies
1.6k
views
Looking for Batch effects in PCA
batch effect pca
2.8 years ago K ▴ 50
2
votes
2
replies
360
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 2.9 years ago by 32k • written 2.9 years ago by ▴ 10
3
votes
6
replies
2.6k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 3.0 years ago by 56k • written 3.0 years ago by ▴ 90
1
vote
2
replies
585
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
3.0 years ago JoannaF ▴ 10
1
vote
3
replies
1.5k
views
PCA from TPM
pca tpm tximport
3.5 years ago tanyabioinfo ▴ 20
0
votes
3
replies
1.3k
views
PCA plot for TPM data
PCA
updated 3.5 years ago by ▴ 60 • written 3.5 years ago by ▴ 20
11
votes
1
reply
3.1k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 3.6 years ago by 32k • written 3.6 years ago by ▴ 60
9
votes
2
replies
665
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 3.6 years ago by ▴ 110 • written 3.6 years ago by 7.6k
0
votes
6
replies
978
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
3.6 years ago lirongrossmann ▴ 60
2
votes
3
replies
710
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 3.6 years ago by ★ 3.8k • written 3.6 years ago by ▴ 20
0
votes
8
replies
3.2k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
3.8 years ago pkachroo ▴ 10
9
votes
7
replies
7.4k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 3.9 years ago by ▴ 10 • written 3.9 years ago by ▴ 30
0
votes
1
reply
492
views
pca plot for tissues and protein values
pca
updated 3.9 years ago by 56k • written 3.9 years ago by ▴ 40
0
votes
0
replies
616
views
gage pca loadings
pca gage loadings
4.1 years ago MT • 0
2
votes
2
replies
650
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 4.2 years ago by 56k • written 4.2 years ago by ▴ 10
4
votes
5
replies
4.3k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
4.4 years ago wd ▴ 30
1
vote
2
replies
796
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 4.5 years ago by ▴ 110 • written 4.5 years ago by • 0
0
votes
1
reply
1.0k
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 4.5 years ago by 32k • written 4.5 years ago by ▴ 10
4
votes
5
replies
1.4k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 4.6 years ago by ▴ 610 • written 4.6 years ago by ▴ 10
2
votes
2
replies
607
views
Insert PCA in design model for adjusting
PCA
updated 4.6 years ago by 56k • written 4.6 years ago by ▴ 10
0
votes
0
replies
493
views
group vectors around pca origins into 5 degrees arc cluster
pca plotpca
4.6 years ago marianarochadesouza • 0
0
votes
7
replies
858
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 4.8 years ago by 32k • written 4.8 years ago by ▴ 40
4
votes
6
replies
562
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 4.9 years ago by 7.6k • written 4.9 years ago by • 0
1
vote
6
replies
809
views
DESEQ2 blocking design doesn't match expectation !
deseq2 block pca
4.9 years ago akp • 0
3
votes
2
replies
673
views
How to find genes causing the high variance of one replicate in the PCA
pca variance deseq2 gene_id
updated 4.9 years ago by 32k • written 4.9 years ago by ▴ 10
1
vote
5
replies
2.1k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
4.9 years ago Peter Alto ▴ 10
4
votes
4
replies
1.9k
views
How to generate a PCA scree plot in DESeq2?
pca deseq2 PCA scree plot
4.9 years ago CandiceChuDVM ▴ 30
74 results • Page 1 of 2
Recent ...
Replies
Comment: DEseq2 nested multi factor no replicates by melissa.mageroy • 0
Thanks for the suggestion!
Comment: Need help in running GO analysis by Rishav ▴ 10
Yes, I already solved that problem. I understand what was the problem . Thank you so much for your time
Answer: DESeq2 ashr with and without reflevels generate different log2FoldChanges by Michael Love 32k
*"How is it possible to get different log2FC using lfcShrink (ashr) by defining relevels compared to no relevels defining?"* This has be…
Comment: After having the output from SingleR for cell type annotation, what's the next s by sofiagreen72211 ▴ 10
I believe, you have a seurat object with 3 groups with barcodes. If this is the case, it's straight forward, get singleR predictions on eac…
Comment: Cannot install packages by BiocManager::install() by FairerBadge66 • 0
Thank you very much, it works, I was loosing my mind already.
Votes
Answer: Need help in running GO analysis
Answer: how can I annotate my scRNAseq clusters from a Rat experiment?
Answer: how can I annotate my scRNAseq clusters from a Rat experiment?
Comment: Cannot install packages by BiocManager::install()
Comment: Unable to install packages on MacOS
Awards • All
Scholar to Guido Hooiveld ★ 2.9k
Teacher to Aaron Lun ★ 26k
Popular Question to Henrik Bengtsson ★ 2.4k
Teacher to Gordon Smyth 42k
Scholar to Martin Morgan 25k
Locations • All
United States, 1 minute ago
China, 2 minutes ago
United States, 12 minutes ago
Sweden, 13 minutes ago
Wageningen University, Wageningen, the Netherlands, 22 minutes ago
Traffic: 481 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