Showing : pca • reset
11
votes
1
reply
4.7k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
9
votes
2
replies
880
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 4.6 years ago by ▴ 110 • written 4.6 years ago by 7.8k
9
votes
5
replies
4.3k
views
DESeq2 PCA different from Prcomp PCA
deseq2 Prcomp PCA
updated 6.1 years ago by 37k • written 6.1 years ago by ▴ 10
9
votes
7
replies
8.5k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 30
6
votes
4
replies
2.5k
views
How to generate a PCA scree plot in DESeq2?
pca deseq2 PCA scree plot
6.0 years ago CandiceChuDVM ▴ 40
5
votes
7
replies
2.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 9 months ago by ★ 4.4k • written 6.6 years ago by ▴ 20
4
votes
5
replies
1.9k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 5.6 years ago by ▴ 610 • written 5.6 years ago by ▴ 10
4
votes
5
replies
454
views
DEseq2 results
heatmaps DEGs PCA
updated 14 months ago by 3.5k • written 14 months ago by • 0
4
votes
6
replies
806
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 5.9 years ago by 7.8k • written 5.9 years ago by • 0
4
votes
2
replies
2.5k
views
PCA for voom normalized RNAseq data
voom pca
updated 7.1 years ago by ★ 27k • written 7.1 years ago by ▴ 120
4
votes
1
reply
2.5k
views
PCA plot on DE genes do not separate samples. DESeq2.
deseq2 pca
updated 6.1 years ago by 59k • written 6.1 years ago by ▴ 10
4
votes
5
replies
4.8k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
5.5 years ago wd ▴ 30
4
votes
5
replies
388
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
2.3 years ago svlachavas ▴ 780
4
votes
1
reply
9.7k
views
Deseq2 PCA plot customize
deseq2 pca
updated 6.4 years ago by 37k • written 6.4 years ago by ▴ 40
3
votes
3
replies
1.2k
views
How to define an outlier array from PCA?
microarray PCA outliers sample outliers limma
updated 6.3 years ago by ★ 27k • written 6.3 years ago by ▴ 60
3
votes
15
replies
1.2k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 17 months ago by 3.5k • written 17 months ago by ▴ 10
3
votes
2
replies
907
views
How to find genes causing the high variance of one replicate in the PCA
pca variance deseq2 gene_id
updated 5.9 years ago by 37k • written 5.9 years ago by ▴ 10
3
votes
4
replies
162
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
updated 24 days ago by ★ 1.0k • written 24 days ago by • 0
3
votes
1
reply
1.5k
views
does pca assume no heteroscedasticity?
deseq2 pca
updated 6.3 years ago by 37k • written 6.3 years ago by ▴ 90
3
votes
5
replies
287
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
12 weeks ago • updated 21 days ago 9906201a • 0
3
votes
6
replies
3.7k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 4.0 years ago by 59k • written 4.0 years ago by ▴ 90
2
votes
16
replies
2.6k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 6.2 years ago by 37k • written 6.2 years ago by ▴ 10
2
votes
2
replies
506
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 4.0 years ago by 37k • written 4.0 years ago by ▴ 10
2
votes
3
replies
892
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 4.7 years ago by ★ 4.4k • written 4.7 years ago by ▴ 20
2
votes
1
reply
2.8k
views
PCA from deseq and r function differ
deseq2 pca
updated 6.5 years ago by 37k • written 6.5 years ago by ▴ 60
2
votes
4
replies
7.8k
views
DESeq2 PCA plot: paired analysis
deseq2 pca
6.3 years ago g.atla ▴ 10
2
votes
4
replies
627
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 5 months ago by ▴ 10 • written 21 months ago by ▴ 100
2
votes
2
replies
797
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 5.2 years ago by 59k • written 5.2 years ago by ▴ 10
2
votes
2
replies
2.1k
views
DESeq2 transformation to use for PCA plot
deseq2 pca rlog transformation variancestabilizingtransformation
6.0 years ago Shobana Sekar ▴ 20
2
votes
6
replies
3.1k
views
PCA in DESeq2 - Can I get the genes contributing most to each component?
deseq2 pca
6.0 years ago Emily ▴ 10
2
votes
6
replies
2.5k
views
Plot PCA with ellipses
pca
updated 2.1 years ago by 37k • written 2.1 years ago by ▴ 40
2
votes
2
replies
129
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 8 weeks ago by 45k • written 8 weeks ago by ▴ 60
2
votes
1
reply
1.5k
views
biplot diagram of PCA analysis differs from plot of variables
r pca biplot
updated 6.9 years ago by 59k • written 6.9 years ago by • 0
2
votes
8
replies
1.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.9 years ago by 37k • written 2.9 years ago by ▴ 10
2
votes
2
replies
742
views
Insert PCA in design model for adjusting
PCA
updated 5.6 years ago by 59k • written 5.6 years ago by ▴ 10
2
votes
1
reply
692
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
1
vote
1
reply
971
views
DeSeq help with PCA
deseq2 PCA
updated 6.6 years ago by 37k • written 6.6 years ago by • 0
1
vote
4
replies
6.3k
views
Error in PCA analysis and with ggbiplot function
bioconductor pca ggbiplot expresiondataset
updated 7.3 years ago by 59k • written 7.3 years ago by ▴ 780
1
vote
5
replies
9.4k
views
How do I extract the principal components in DESeq2?
deseq2 pca
updated 6.9 years ago by 37k • written 6.9 years ago by ▴ 10
1
vote
2
replies
674
views
nice 3D displays for PCA analysis
PCA
updated 6.0 years ago by 59k • written 6.0 years ago by ▴ 640
1
vote
5
replies
2.7k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
5.9 years ago Peter Alto ▴ 10
1
vote
6
replies
1.0k
views
DESEQ2 blocking design doesn't match expectation !
deseq2 block pca
5.9 years ago akp • 0
1
vote
2
replies
975
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 5.5 years ago by ▴ 140 • written 5.5 years ago by • 0
1
vote
3
replies
2.5k
views
PCA from TPM
pca tpm tximport
4.6 years ago tanyabioinfo ▴ 20
1
vote
2
replies
997
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
4.1 years ago JoannaF ▴ 10
1
vote
3
replies
468
views
Deseq2 PCA Anlysis
deseq2 pca
updated 3.2 years ago by 37k • written 3.2 years ago by • 0
1
vote
1
reply
436
views
PCA axis description SNPRelate
SNPRelate PCA
updated 3.2 years ago by ▴ 820 • written 3.2 years ago by ▴ 60
1
vote
4
replies
446
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 2.6 years ago by 37k • written 2.6 years ago by ▴ 50
1
vote
1
reply
201
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 2.2 years ago by ★ 4.4k • written 2.2 years ago by • 0
1
vote
4
replies
2.1k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 20 months ago by 45k • written 20 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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