Showing : pca • reset
0
votes
2
replies
119
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
5 weeks ago Clara • 0
4
votes
5
replies
248
views
DEseq2 results
heatmaps DEGs PCA
updated 4 months ago by 3.2k • written 4 months ago by • 0
1
vote
1
reply
156
views
Diffbind principal components
PCA DiffBind
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
3
votes
15
replies
675
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 7 months ago by 3.2k • written 7 months ago by ▴ 10
0
votes
1
reply
219
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 8 months ago by 3.2k • written 8 months ago by • 0
0
votes
10
replies
453
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 8 months ago by 33k • written 8 months ago by ▴ 10
0
votes
0
replies
125
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
9 months ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
556
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 10 months ago by 43k • written 10 months ago by • 0
2
votes
3
replies
286
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 11 months ago by 3.2k • written 11 months ago by ▴ 100
0
votes
1
reply
125
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
15 months ago cupret • 0
2
votes
6
replies
1.1k
views
Plot PCA with ellipses
pca
updated 15 months ago by 33k • written 15 months ago by ▴ 40
0
votes
1
reply
118
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 16 months ago by 3.2k • written 16 months ago by • 0
1
vote
1
reply
100
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 16 months ago by ★ 4.0k • written 16 months ago by • 0
4
votes
5
replies
213
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
17 months ago svlachavas ▴ 780
1
vote
4
replies
290
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 21 months ago by 33k • written 21 months ago by ▴ 50
1
vote
8
replies
774
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.1 years ago by 33k • written 2.1 years ago by • 0
0
votes
2
replies
293
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.3 years ago by ★ 27k • written 2.3 years ago by ▴ 10
1
vote
1
reply
276
views
PCA axis description SNPRelate
SNPRelate PCA
updated 2.3 years ago by ▴ 800 • written 2.3 years ago by ▴ 60
1
vote
3
replies
329
views
Deseq2 PCA Anlysis
deseq2 pca
updated 2.4 years ago by 33k • written 2.4 years ago by • 0
0
votes
1
reply
653
views
PCA analysis with 2 biological replicates
bayseq PCA
2.4 years ago bsad • 0
0
votes
3
replies
487
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 2.6 years ago by 33k • written 2.6 years ago by ▴ 40
2
votes
1
reply
493
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 2.6 years ago by ★ 27k • written 2.6 years ago by • 0
0
votes
0
replies
385
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
2.7 years ago kbobowik • 0
0
votes
7
replies
655
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
0
votes
3
replies
1.6k
views
Looking for Batch effects in PCA
batch effect pca
3.0 years ago K ▴ 50
2
votes
2
replies
403
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 3.1 years ago by 33k • written 3.1 years ago by ▴ 10
3
votes
6
replies
2.9k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 3.2 years ago by 57k • written 3.2 years ago by ▴ 90
1
vote
2
replies
679
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
3.3 years ago JoannaF ▴ 10
1
vote
3
replies
1.7k
views
PCA from TPM
pca tpm tximport
3.8 years ago tanyabioinfo ▴ 20
0
votes
3
replies
1.5k
views
PCA plot for TPM data
PCA
updated 3.8 years ago by ▴ 60 • written 3.8 years ago by ▴ 20
11
votes
1
reply
3.5k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 3.8 years ago by 33k • written 3.8 years ago by ▴ 60
9
votes
2
replies
708
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 3.8 years ago by ▴ 110 • written 3.8 years ago by 7.6k
0
votes
6
replies
1.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
3.8 years ago lirongrossmann ▴ 60
2
votes
3
replies
756
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 3.8 years ago by ★ 4.0k • written 3.9 years ago by ▴ 20
0
votes
8
replies
3.4k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
4.0 years ago pkachroo ▴ 10
9
votes
7
replies
7.6k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by ▴ 30
0
votes
1
reply
522
views
pca plot for tissues and protein values
pca
updated 4.2 years ago by 57k • written 4.2 years ago by ▴ 40
0
votes
0
replies
657
views
gage pca loadings
pca gage loadings
4.3 years ago MT ▴ 10
2
votes
2
replies
684
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 4.4 years ago by 57k • written 4.4 years ago by ▴ 10
4
votes
5
replies
4.5k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
4.7 years ago • updated 4.6 years ago wd ▴ 30
1
vote
2
replies
841
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 4.7 years ago by ▴ 110 • written 4.7 years ago by • 0
0
votes
1
reply
1.1k
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 4.7 years ago by 33k • written 4.7 years ago by ▴ 10
4
votes
5
replies
1.5k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 4.8 years ago by ▴ 610 • written 4.8 years ago by ▴ 10
2
votes
2
replies
652
views
Insert PCA in design model for adjusting
PCA
updated 4.8 years ago by 57k • written 4.8 years ago by ▴ 10
0
votes
0
replies
522
views
group vectors around pca origins into 5 degrees arc cluster
pca plotpca
4.8 years ago marianarochadesouza • 0
0
votes
7
replies
950
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 5.1 years ago by 33k • written 5.1 years ago by ▴ 40
4
votes
6
replies
610
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 5.1 years ago by 7.6k • written 5.1 years ago by • 0
1
vote
6
replies
876
views
DESEQ2 blocking design doesn't match expectation !
deseq2 block pca
5.1 years ago akp • 0
3
votes
2
replies
727
views
How to find genes causing the high variance of one replicate in the PCA
pca variance deseq2 gene_id
updated 5.1 years ago by 33k • written 5.1 years ago by ▴ 10
1
vote
5
replies
2.2k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
5.1 years ago Peter Alto ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I wonder what would be a good metric to assess the quantification quality
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for sharing your thoughts. I used Salmon and indexed using hg38 gencodes transcriptome. After the tximport step, I ended up gett…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx so much for the diagnosis and advice. Indeed, in my data, some genes have all 0 for all sampes of a contrast for both "Mut" and "WT" gr…
Comment: Best practice for quantifying sncRNA by Steve Lianoglou 13k
> It's my opinion that miRNA is a mirage intended to make MDs salivate and biostatisticians wail in misery, but what do I know? I'll tell …
Comment: Idea: Using DESeq2 to test a change in ratio of two genes by Michael Love 33k
Yes, it's true that we take the reference gene(s) as a noise free measurement of the reference variation with this approach, and control ag…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Awards • All
Popular Question to amalthomas111 • 0
Scholar to gabriel.hoffman ▴ 90
Popular Question to Thomas Maurel ▴ 790
Scholar to James W. MacDonald 57k
Teacher to Guido Hooiveld ★ 3.0k
Locations • All
Australia, 12 minutes ago
The city by the bay, 1 hour ago
Republic of Ireland, 1 hour ago
Australia, 1 hour ago
United States, 2 hours ago
Traffic: 759 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