Showing : pca • reset
0
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2
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140
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 14 days ago by ▴ 970 • written 14 days ago by • 0
1
vote
1
reply
164
views
mixOmics 3D scatterplot for individuals not displaying
plotIndiv 3D mixOmics PCA
7 weeks ago • updated 6 weeks ago Blobby123 • 0
0
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2
replies
221
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
7 months ago Clara • 0
4
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5
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392
views
DEseq2 results
heatmaps DEGs PCA
updated 11 months ago by 3.4k • written 11 months ago by • 0
1
vote
1
reply
249
views
Diffbind principal components
PCA DiffBind
updated 11 months ago by ★ 4.3k • written 11 months ago by • 0
3
votes
15
replies
968
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
391
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
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10
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680
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Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 15 months ago by 35k • written 15 months ago by ▴ 10
0
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0
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201
views
contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
15 months ago Assa Yeroslaviz ★ 1.5k
1
vote
4
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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
494
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 6 weeks ago by ▴ 10 • written 17 months ago by ▴ 100
0
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1
reply
325
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
219
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
171
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
328
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
394
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
378
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
383
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
427
views
Deseq2 PCA Anlysis
deseq2 pca
updated 2.9 years ago by 35k • written 2.9 years ago by • 0
0
votes
1
reply
861
views
PCA analysis with 2 biological replicates
bayseq PCA
2.9 years ago bsad • 0
0
votes
3
replies
645
views
Uncertain about PCA plot for DESeq2 analysis
deseq2 pca bioconductor rnaseq
updated 3.1 years ago by 35k • written 3.1 years ago by ▴ 40
2
votes
1
reply
627
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
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0
replies
503
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
3.2 years ago kbobowik • 0
0
votes
7
replies
791
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
464
views
DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
DESEq2 PCA
updated 3.7 years ago by 35k • written 3.7 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
855
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
4.3 years ago tanyabioinfo ▴ 20
0
votes
3
replies
1.9k
views
PCA plot for TPM data
PCA
updated 4.3 years ago by ▴ 60 • written 4.3 years ago by ▴ 20
11
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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
812
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
4.4 years ago • updated 4.3 years ago lirongrossmann ▴ 60
2
votes
3
replies
832
views
Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
diffbind PCA
updated 4.4 years ago by ★ 4.3k • written 4.4 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
576
views
pca plot for tissues and protein values
pca
updated 4.7 years ago by 58k • written 4.7 years ago by ▴ 40
0
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0
replies
713
views
gage pca loadings
pca gage loadings
4.8 years ago MT ▴ 10
2
votes
2
replies
758
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
5.2 years ago • updated 5.1 years ago wd ▴ 30
1
vote
2
replies
932
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 5.2 years ago by ▴ 130 • written 5.2 years ago by • 0
0
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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
705
views
Insert PCA in design model for adjusting
PCA
updated 5.3 years ago by 58k • written 5.3 years ago by ▴ 10
0
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0
replies
584
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 5.6 years ago by 35k • written 5.6 years ago by ▴ 40
4
votes
6
replies
759
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: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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