Showing : PCA • reset
2
votes
16
replies
3.6k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
8
votes
15
replies
1.5k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago IUH • 0
3
votes
15
replies
3.2k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by ▴ 10
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 42k • written 12 months ago by ▴ 10
0
votes
10
replies
1.7k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 3.5 years ago by 42k • written 3.5 years ago by ▴ 10
2
votes
8
replies
3.3k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 4.9 years ago by 42k • written 4.9 years ago by ▴ 10
0
votes
8
replies
6.6k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
6.8 years ago pkachroo ▴ 10
0
votes
7
replies
1.7k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 7.8 years ago by 42k • written 7.8 years ago by ▴ 40
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
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
5
votes
7
replies
3.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 2.7 years ago by ★ 5.2k • written 8.5 years ago by ▴ 20
1
vote
6
replies
1.5k
views
DESEQ2 blocking design doesn't match expectation !
deseq2 block pca
7.9 years ago akp • 0
4
votes
6
replies
1.4k
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 7.8 years ago by ★ 7.9k • written 7.9 years ago by • 0
3
votes
6
replies
4.9k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 110
0
votes
6
replies
3.2k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.6 years ago lirongrossmann ▴ 80
2
votes
6
replies
5.6k
views
PCA in DESeq2 - Can I get the genes contributing most to each component?
deseq2 pca
8.0 years ago Emily ▴ 10
2
votes
6
replies
7.2k
views
Plot PCA with ellipses
pca
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 60
4
votes
5
replies
2.8k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 7.6 years ago by ▴ 650 • written 7.6 years ago by ▴ 10
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.5 years ago by ▴ 20
4
votes
5
replies
13k
views
How do I extract the principal components in DESeq2?
deseq2 pca
updated 8.8 years ago by 42k • written 8.8 years ago by ▴ 10
4
votes
5
replies
6.6k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
7.4 years ago wd ▴ 30
1
vote
5
replies
3.7k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
7.9 years ago Peter Alto ▴ 10
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
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 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
2.2 years ago • updated 2.0 years ago 9906201a ▴ 20
9
votes
5
replies
5.7k
views
DESeq2 PCA different from Prcomp PCA
deseq2 Prcomp PCA
updated 8.1 years ago by 42k • written 8.1 years ago by ▴ 10
4
votes
5
replies
2.1k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.0 years ago by • 0
2
votes
4
replies
7.0k
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
8.9k
views
DESeq2 PCA plot: paired analysis
deseq2 pca
8.3 years ago g.atla ▴ 10
2
votes
4
replies
1.6k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 2.4 years ago by ▴ 10 • written 3.7 years ago by ▴ 120
1
vote
4
replies
1.4k
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
6
votes
4
replies
3.9k
views
How to generate a PCA scree plot in DESeq2?
pca deseq2 PCA scree plot
7.9 years ago CandiceChuDVM ▴ 40
0
votes
4
replies
16k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 9.1 years ago by 42k • written 9.1 years ago by ▴ 60
1
vote
4
replies
3.5k
views
Looking for Batch effects in PCA
batch effect pca
5.8 years ago • updated 15 months ago KB ▴ 50
1
vote
4
replies
8.2k
views
Error in PCA analysis and with ggbiplot function
bioconductor pca ggbiplot expresiondataset
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 830
0
votes
3
replies
3.1k
views
How to change the dot size in plotPCA?
plotPCA PCA
updated 13 months ago by • 0 • written 13 months ago by • 0
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 ★ 5.2k • written 6.6 years ago by ▴ 20
3
votes
3
replies
1.6k
views
How to define an outlier array from PCA?
microarray PCA outliers sample outliers limma
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 60
0
votes
3
replies
1.8k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 5.3 years ago by 42k • written 5.3 years ago by ▴ 40
0
votes
3
replies
371
views
Biplot has a secondary x-axis and y-axis
pcaMethods pca
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
1
vote
3
replies
1.0k
views
Deseq2 PCA Anlysis
deseq2 pca
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
0
votes
3
replies
1.5k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
8.0 years ago newsomew13 • 0
1
vote
3
replies
4.5k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
0
votes
3
replies
2.0k
views
Query about DEXSeq
dexseq batch effect PCA
8.7 years ago n.deshpande • 0
2
votes
2
replies
3.1k
views
DESeq2 transformation to use for PCA plot
deseq2 pca rlog transformation variancestabilizingtransformation
8.0 years ago Shobana Sekar ▴ 20
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 5.9 years ago by 42k • written 5.9 years ago by ▴ 10
0
votes
2
replies
905
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
0
votes
2
replies
1.6k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by • 0
1
vote
2
replies
2.9k
views
DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq pca pasilla
updated 8.2 years ago by ▴ 150 • written 8.2 years ago by • 0
2
votes
2
replies
1.1k
views
Insert PCA in design model for adjusting
PCA
updated 7.6 years ago by 65k • written 7.6 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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