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PCa
•
reset
0
votes
0
replies
91
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
19 days ago
feather-W
• 0
0
votes
3
replies
313
views
Biplot has a secondary x-axis and y-axis
pcaMethods
pca
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
yousavdj
• 0
8
votes
15
replies
1.4k
views
PCA percent variance DESeq2
PCA
DESeq2
8 months ago • updated 7 months ago
IUH
• 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 12 months ago by
Michael Love
41k • written 12 months ago by
urwah
▴ 10
0
votes
3
replies
2.9k
views
How to change the dot size in plotPCA?
plotPCA
PCA
updated 12 months ago by
hediatnani
• 0 • written 13 months ago by
Yijing
• 0
0
votes
1
reply
416
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 13 months ago by
Basti
▴ 760 • written 13 months ago by
fuqichen1
• 0
0
votes
2
replies
824
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 13 months ago by
swbarnes2
★ 1.3k • written 13 months ago by
mbxdn1
• 0
1
vote
1
reply
930
views
PCA input data from DRAGEN RNA pipeline
illumina
PCAtools
PCA
updated 17 months ago by
Kevin Blighe
★ 3.9k • written 17 months ago by
ilaria.debenedictis
• 0
4
votes
5
replies
2.0k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 24 months ago by
960942
• 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
Gordon Smyth
50k • written 2.1 years ago by
Raito92
▴ 60
0
votes
0
replies
559
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom
PCA
LEA
2.1 years ago
Bruna
• 0
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
2.1 years ago • updated 23 months ago
9906201a
▴ 20
0
votes
2
replies
1.5k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2
PCA
updated 2.3 years ago by
swbarnes2
★ 1.3k • written 2.3 years ago by
Jonas
• 0
1
vote
1
reply
848
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv
3D
mixOmics
PCA
2.4 years ago
Blobby123
• 0
0
votes
2
replies
1.7k
views
PCA and heatmaps: most variable genes selection
DESeq2
ExpressionData
heatmaps
pca
2.8 years ago
Clara
• 0
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
1
vote
1
reply
774
views
Diffbind principal components
PCA
DiffBind
updated 3.2 years ago by
Rory Stark
★ 5.1k • written 3.2 years ago by
alessandrotestori7
• 0
3
votes
15
replies
3.1k
views
How to ellipse a subset of data PCA biplot?
biplot
PCA
RNASeq
PCAtools
updated 3.3 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
mschmidt
▴ 10
0
votes
1
reply
1.7k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools
biplot
DESeq2
RNASeq
PCA
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
ecg1g15
▴ 20
0
votes
10
replies
1.7k
views
Do I have clustering by library size?
PCA
DESeq2
Normalization
librarysize
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
pkachroo
▴ 10
0
votes
0
replies
664
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave
PCA
3.5 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
4
replies
6.8k
views
Trying to do a PCA using edgeR with expression data
edger
expression data
pca
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
waalkes
• 0
2
votes
4
replies
1.5k
views
Comparing discrete variable to PCA
EDA
pcaExplorer
PCAtools
PCA
updated 2.3 years ago by
Miguel
▴ 10 • written 3.7 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
2.3k
views
Should I normalize read counts if I want to run plotPCA?
deseq2
PCA
4.0 years ago
cupret
• 0
2
votes
6
replies
7.0k
views
Plot PCA with ellipses
pca
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
Matan G.
▴ 60
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
Kevin Blighe
★ 3.9k • written 4.1 years ago by
ecg1g15
▴ 20
1
vote
1
reply
709
views
DiffBind in depth explanation
DiffBind
PCA
Differential Analysis
updated 4.1 years ago by
Rory Stark
★ 5.1k • written 4.1 years ago by
jrp208
• 0
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
1
vote
4
replies
1.4k
views
Difference in PCA variance calculation in DESeq2
deseq2
pca
hclust
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
ag1805x
▴ 80
2
votes
8
replies
3.2k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
bioyas
▴ 10
0
votes
2
replies
884
views
diffHic ICE normalization PCA with NAs
diffHic
normalization
pca
NAs
HI-C
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
inzirio
▴ 10
1
vote
1
reply
961
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 5.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
serpalma.v
▴ 60
1
vote
3
replies
991
views
Deseq2 PCA Anlysis
deseq2
pca
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
sherajilir
• 0
0
votes
1
reply
2.4k
views
PCA analysis with 2 biological replicates
bayseq
PCA
5.1 years ago
bsad
• 0
0
votes
3
replies
1.8k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2
pca
bioconductor
rnaseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
pepere
▴ 40
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater
pca
features
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
jws
• 0
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq
edaseq
pca
5.4 years ago
kbobowik
• 0
0
votes
7
replies
1.5k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2
sizefactors
pca
normalization
library size factor
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
ipso
• 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
2
votes
2
replies
1.2k
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
Michael Love
41k • written 5.9 years ago by
JoannaF
▴ 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
James W. MacDonald
65k • written 6.0 years ago by
Biologist
▴ 110
1
vote
2
replies
1.7k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2
PCA
rlog transformation
biotype
6.0 years ago
JoannaF
▴ 10
1
vote
3
replies
4.4k
views
PCA from TPM
pca
tpm
tximport
6.5 years ago
tanyabioinfo
▴ 20
0
votes
5
replies
3.7k
views
PCA plot for TPM data
PCA
written 6.5 years ago by
tanyabioinfo
▴ 20
12
votes
1
reply
7.1k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
lirongrossmann
▴ 80
9
votes
2
replies
1.6k
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
Vegard Nygaard
▴ 110 • written 6.5 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
6.6 years ago
lirongrossmann
▴ 80
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
Rory Stark
★ 5.1k • written 6.6 years ago by
Gary
▴ 20
0
votes
8
replies
6.6k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2
PCA
batch effect
6.7 years ago
pkachroo
▴ 10
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
Kushal K Dey
▴ 10 • written 6.8 years ago by
s.w.vanderlaan
▴ 30
50 results • Page
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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