Showing : PCA • reset
0
votes
2
replies
111
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 8 days ago by ▴ 970 • written 8 days ago by • 0
1
vote
1
reply
161
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
6 weeks ago Blobby123 • 0
0
votes
2
replies
216
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
7 months ago Clara • 0
4
votes
5
replies
389
views
DEseq2 results
heatmaps DEGs PCA
updated 10 months ago by 3.4k • written 10 months ago by • 0
1
vote
1
reply
247
views
Diffbind principal components
PCA DiffBind
updated 11 months ago by ★ 4.3k • written 11 months ago by • 0
3
votes
15
replies
961
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 13 months ago by 3.4k • written 13 months ago by ▴ 10
0
votes
1
reply
384
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 14 months ago by 3.4k • written 14 months ago by • 0
0
votes
10
replies
679
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 14 months ago by 35k • written 14 months ago by ▴ 10
0
votes
0
replies
199
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
15 months ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
1.4k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 16 months ago by 44k • written 16 months ago by • 0
2
votes
4
replies
488
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 5 weeks ago by ▴ 10 • written 17 months ago by ▴ 100
0
votes
1
reply
314
views
Should I normalize read counts if I want to run plotPCA?
deseq2 PCA
21 months ago cupret • 0
2
votes
6
replies
1.9k
views
Plot PCA with ellipses
pca
updated 21 months ago by 35k • written 21 months ago by ▴ 40
0
votes
1
reply
214
views
How do you know if your DESeq2 data has normal distribution?
R pca ellipse normaldistribution
updated 22 months ago by 3.4k • written 22 months ago by • 0
1
vote
1
reply
168
views
DiffBind in depth explanation
DiffBind PCA Differential Analysis
updated 22 months ago by ★ 4.3k • written 22 months ago by • 0
4
votes
5
replies
324
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
23 months ago svlachavas ▴ 780
1
vote
4
replies
389
views
Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 2.3 years ago by 35k • written 2.3 years ago by ▴ 50
1
vote
8
replies
1.0k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.6 years ago by 35k • written 2.6 years ago by • 0
0
votes
2
replies
377
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 10
1
vote
1
reply
377
views
PCA axis description SNPRelate
SNPRelate PCA
updated 2.8 years ago by ▴ 820 • written 2.8 years ago by ▴ 60
1
vote
3
replies
423
views
Deseq2 PCA Anlysis
deseq2 pca
updated 2.8 years ago by 35k • written 2.8 years ago by • 0
0
votes
1
reply
852
views
PCA analysis with 2 biological replicates
bayseq PCA
2.8 years ago bsad • 0
0
votes
3
replies
639
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 3.0 years ago by 35k • written 3.0 years ago by ▴ 40
2
votes
1
reply
619
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 3.1 years ago by ★ 27k • written 3.1 years ago by • 0
0
votes
0
replies
497
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
3.2 years ago kbobowik • 0
0
votes
7
replies
785
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 3.4 years ago by 35k • written 3.4 years ago by • 0
0
votes
3
replies
1.9k
views
Looking for Batch effects in PCA
batch effect pca
3.5 years ago K ▴ 50
2
votes
2
replies
461
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 3.6 years ago by 35k • written 3.6 years ago by ▴ 10
3
votes
6
replies
3.4k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 3.7 years ago by 58k • written 3.7 years ago by ▴ 90
1
vote
2
replies
847
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
3.8 years ago JoannaF ▴ 10
1
vote
3
replies
2.2k
views
PCA from TPM
pca tpm tximport
4.2 years ago tanyabioinfo ▴ 20
0
votes
3
replies
1.9k
views
PCA plot for TPM data
PCA
updated 4.2 years ago by ▴ 60 • written 4.2 years ago by ▴ 20
11
votes
1
reply
4.2k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 60
9
votes
2
replies
807
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 4.3 years ago by ▴ 110 • written 4.3 years ago by 7.7k
0
votes
6
replies
1.3k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
4.3 years ago lirongrossmann ▴ 60
2
votes
3
replies
829
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 4.3 years ago by ★ 4.3k • written 4.3 years ago by ▴ 20
0
votes
8
replies
3.8k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
4.5 years ago pkachroo ▴ 10
9
votes
7
replies
8.1k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by ▴ 30
0
votes
1
reply
573
views
pca plot for tissues and protein values
pca
updated 4.7 years ago by 58k • written 4.7 years ago by ▴ 40
0
votes
0
replies
711
views
gage pca loadings
pca gage loadings
4.8 years ago MT ▴ 10
2
votes
2
replies
754
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 4.9 years ago by 58k • written 4.9 years ago by ▴ 10
4
votes
5
replies
4.7k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
5.1 years ago wd ▴ 30
1
vote
2
replies
931
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by • 0
0
votes
1
reply
1.3k
views
how to plot PCA for only one of two groups compared or plot three groups at a time
deseq2 bioconductor rna-seq pca
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 10
4
votes
5
replies
1.8k
views
SVA and proportion of variance explained
sva svd explained variance pca
updated 5.3 years ago by ▴ 610 • written 5.3 years ago by ▴ 10
2
votes
2
replies
702
views
Insert PCA in design model for adjusting
PCA
updated 5.3 years ago by 58k • written 5.3 years ago by ▴ 10
0
votes
0
replies
581
views
group vectors around pca origins into 5 degrees arc cluster
pca plotpca
5.3 years ago marianarochadesouza • 0
0
votes
7
replies
1.0k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 5.5 years ago by 35k • written 5.5 years ago by ▴ 40
4
votes
6
replies
749
views
Characterization of simultaneous transcription factors over expression
deseq2 factominer PCA
updated 5.6 years ago by 7.7k • written 5.6 years ago by • 0
1
vote
6
replies
981
views
DESEQ2 blocking design doesn't match expectation !
deseq2 block pca
5.6 years ago akp • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep)) by tjhwangxiong • 0
``` https://drive.google.com/drive/folders/1787thVatZpt_KFrfXY-aXV1m0FRm8Mhm?usp=sharing ``` Thanks for your reply. I have uploaded the fil…
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
No I can’t help with exercises. Just to be clear I’m not affiliated with Harvard and have no supported effort in relation to the edx classe…
Answer: Problems to find the pvalues via rowttests by Gordon Smyth 44k
Ordinary t-tests aren't recommended for genomic analyses because they have poor power and higher false discovery rates. Using the limma p…
Answer: How to insert a qvalues column in a dataframe with pvalues in R by Gordon Smyth 44k
Here and in a previous post, it seems you're not using recommended Bioconductor workflows for Affymetrix microarrays. If you used a standar…
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
Thank you. I hope I can still let you know if I have issues with your exercises. They are very challenging but useful! :)
Votes
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
plyranges select() when a metadata column is shared with core variable
Awards • All
Popular Question to Gordon Smyth 44k
Popular Question to floriandeckert ▴ 30
Popular Question to mikhael.manurung ▴ 230
Popular Question to Stephanie M. Gogarten ▴ 820
Teacher to Aaron Lun ★ 27k
Locations • All
Portugal, 31 minutes ago
United States, 35 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
MSKCC | New York, NY, 1 hour ago
United Kingdom, 1 hour ago
Traffic: 228 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6