Showing : pca • reset
0
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130
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
9 weeks ago feather-W • 0
0
votes
3
replies
438
views
Biplot has a secondary x-axis and y-axis
pcaMethods pca
updated 3 months ago by 66k • written 3 months ago by • 0
8
votes
15
replies
1.6k
views
PCA percent variance DESeq2
PCA DESeq2
9 months ago IUH • 0
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 13 months ago by 42k • written 13 months ago by ▴ 10
0
votes
3
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3.4k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
456
views
How to extract proteins from PCs in plot_pca in DEP package
DEP PrincipalComponent PCA plot_pca
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
2
replies
887
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2 Galaxy pca
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
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1
reply
1.0k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 18 months ago by ★ 3.9k • written 18 months ago by • 0
4
votes
5
replies
2.2k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.1 years ago by • 0
2
votes
2
replies
1.3k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 60
0
votes
0
replies
586
views
LEA package (3.6.0): tracy-widom test problems
tracy-widom PCA LEA
2.2 years ago Bruna • 0
5
votes
5
replies
1.7k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.3 years ago • updated 2.1 years ago 9906201a ▴ 20
0
votes
2
replies
1.6k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
1
vote
1
reply
886
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
2.5 years ago Blobby123 • 0
0
votes
2
replies
1.7k
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
3.0 years ago Clara ▴ 10
4
votes
5
replies
1.4k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.2 years ago by ★ 3.9k • written 3.3 years ago by • 0
1
vote
1
reply
807
views
Diffbind principal components
PCA DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
3
votes
15
replies
3.2k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by ▴ 20
0
votes
10
replies
1.8k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 3.6 years ago by 42k • written 3.6 years ago by ▴ 10
0
votes
0
replies
689
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
3.6 years ago Assa Yeroslaviz ★ 1.5k
2
votes
4
replies
7.1k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 3.7 years ago by 50k • written 3.7 years ago by • 0
2
votes
4
replies
1.6k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 2.5 years ago by ▴ 20 • written 3.8 years ago by ▴ 120
0
votes
1
reply
2.4k
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
4.1 years ago cupret • 0
2
votes
6
replies
7.4k
views
Plot PCA with ellipses
pca
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 60
2
votes
1
reply
1.1k
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 20
1
vote
1
reply
753
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by • 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
4.3 years ago svlachavas ▴ 830
1
vote
4
replies
1.5k
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 4.6 years ago by 42k • written 4.6 years ago by ▴ 80
2
votes
8
replies
3.4k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 10
0
votes
2
replies
922
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
1
reply
1.0k
views
PCA axis description SNPRelate
SNPRelate PCA
updated 5.2 years ago by ▴ 870 • written 5.2 years ago by ▴ 60
1
vote
3
replies
1.0k
views
Deseq2 PCA Anlysis
deseq2 pca
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
1
reply
2.5k
views
PCA analysis with 2 biological replicates
bayseq PCA
5.2 years ago bsad • 0
0
votes
3
replies
1.8k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 40
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
votes
0
replies
1.3k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.5 years ago kbobowik • 0
0
votes
7
replies
1.6k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
1
vote
4
replies
3.5k
views
Looking for Batch effects in PCA
batch effect pca
5.9 years ago • updated 16 months ago KB ▴ 50
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 6.0 years ago by 42k • written 6.0 years ago by ▴ 10
3
votes
6
replies
4.9k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 6.1 years ago by 66k • written 6.1 years ago by ▴ 110
1
vote
2
replies
1.8k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
6.1 years ago JoannaF ▴ 10
1
vote
3
replies
4.5k
views
PCA from TPM
pca tpm tximport
6.6 years ago tanyabioinfo ▴ 20
0
votes
5
replies
3.9k
views
PCA plot for TPM data
PCA
written 6.6 years ago by ▴ 20
12
votes
1
reply
7.2k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
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 6.6 years ago by ▴ 110 • written 6.6 years ago by ★ 7.9k
0
votes
6
replies
3.2k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.7 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 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 20
0
votes
8
replies
6.7k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
6.9 years ago • updated 6.8 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 6.9 years ago by ▴ 10 • written 6.9 years ago by ▴ 30
50 results • Page 1 of 1
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Replies
Comment: How to compare subset of samples from VCF files by Gordon Smyth 50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files by Marco • 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database by James W. MacDonald 66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database by luigi.faino • 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database by James W. MacDonald 66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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