Showing : pca • reset
2
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3
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1.0k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 3 months ago by • 0
0
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0
replies
352
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 months ago feather-W • 0
0
votes
3
replies
887
views
Biplot has a secondary x-axis and y-axis
pcaMethods pca
updated 8 months ago by 67k • written 8 months ago by • 0
8
votes
15
replies
2.2k
views
PCA percent variance DESeq2
PCA DESeq2
14 months ago IUH • 0
3
votes
12
replies
2.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 18 months ago by 42k • written 18 months ago by ▴ 10
0
votes
3
replies
4.7k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 19 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
593
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 19 months ago by ▴ 780 • written 19 months ago by • 0
0
votes
2
replies
1.1k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
1
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1
reply
1.3k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 24 months ago by ★ 4.0k • written 24 months ago by • 0
4
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5
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2.7k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.5 years ago by • 0
2
votes
2
replies
1.6k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 2.6 years ago by 51k • written 2.6 years ago by ▴ 60
0
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0
replies
711
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
2.7 years ago Bruna • 0
5
votes
5
replies
2.0k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.7 years ago • updated 2.5 years ago 9906201a ▴ 20
0
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2
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1.9k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
1
vote
1
reply
1.0k
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
2.9 years ago Blobby123 • 0
0
votes
2
replies
2.0k
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
3.4 years ago Clara ▴ 10
4
votes
5
replies
1.6k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
1
vote
1
reply
913
views
Diffbind principal components
PCA DiffBind
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
3
votes
15
replies
3.6k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 30
0
votes
10
replies
2.2k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 10
0
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0
replies
814
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
4.1 years ago Assa Yeroslaviz ★ 1.5k
2
votes
4
replies
8.2k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 4.2 years ago by 51k • written 4.2 years ago by • 0
2
votes
4
replies
1.9k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 2.9 years ago by ▴ 20 • written 4.2 years ago by ▴ 120
0
votes
1
reply
2.9k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
4.5 years ago cupret • 0
2
votes
6
replies
9.1k
views
Plot PCA with ellipses
pca
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 60
2
votes
1
reply
1.3k
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 30
1
vote
1
reply
957
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 4.6 years ago by ★ 5.2k • written 4.6 years ago by • 0
4
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5
replies
1.3k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
4.7 years ago svlachavas ▴ 830
1
vote
4
replies
1.7k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 80
2
votes
8
replies
3.7k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 10
0
votes
2
replies
1.1k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 10
1
vote
1
reply
1.1k
views
PCA axis description SNPRelate
SNPRelate PCA
updated 5.6 years ago by ▴ 870 • written 5.6 years ago by ▴ 60
1
vote
3
replies
1.2k
views
Deseq2 PCA Anlysis
deseq2 pca
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
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1
reply
2.9k
views
PCA analysis with 2 biological replicates
bayseq PCA
5.6 years ago bsad • 0
0
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3
replies
2.1k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 40
2
votes
1
reply
1.4k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
0
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0
replies
1.4k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.0 years ago kbobowik • 0
0
votes
7
replies
1.8k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
1
vote
4
replies
3.9k
views
Looking for Batch effects in PCA
batch effect pca
6.3 years ago • updated 21 months ago KB ▴ 50
2
votes
2
replies
1.4k
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 6.4 years ago by 42k • written 6.4 years ago by ▴ 10
3
votes
6
replies
5.2k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 6.5 years ago by 67k • written 6.5 years ago by ▴ 120
1
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2
replies
2.0k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
6.5 years ago JoannaF ▴ 10
1
vote
3
replies
4.9k
views
PCA from TPM
pca tpm tximport
7.0 years ago tanyabioinfo ▴ 20
0
votes
5
replies
4.4k
views
PCA plot for TPM data
PCA
written 7.0 years ago by ▴ 20
12
votes
1
reply
7.7k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 7.0 years ago by 42k • written 7.0 years ago by ▴ 80
9
votes
2
replies
1.9k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 7.0 years ago by ▴ 110 • written 7.1 years ago by ★ 7.9k
0
votes
6
replies
3.6k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
7.1 years ago lirongrossmann ▴ 80
2
votes
3
replies
1.7k
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by ▴ 20
0
votes
8
replies
7.2k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
7.3 years ago pkachroo ▴ 10
50 results • Page 1 of 1
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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Ai • 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2 by icecreamlover • 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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