Showing : pca • reset
0
votes
4
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13k
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3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 7.1 years ago by 37k • written 7.1 years ago by ▴ 50
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
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
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
2
votes
4
replies
7.8k
views
DESeq2 PCA plot: paired analysis
deseq2 pca
6.3 years ago g.atla ▴ 10
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
4
votes
5
replies
4.8k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
5.5 years ago wd ▴ 30
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
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
0
votes
8
replies
4.1k
views
Differences in PCA plot - rld versus vsd normalized data (DESeq2)
deseq2 PCA batch effect
4.8 years ago pkachroo ▴ 10
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
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
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
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
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
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
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
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
1
vote
3
replies
2.5k
views
PCA from TPM
pca tpm tximport
4.6 years ago tanyabioinfo ▴ 20
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
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
2.1k
views
DESeq2 transformation to use for PCA plot
deseq2 pca rlog transformation variancestabilizingtransformation
6.0 years ago Shobana Sekar ▴ 20
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
0
votes
3
replies
2.1k
views
PCA plot for TPM data
PCA
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by ▴ 20
0
votes
3
replies
2.0k
views
Looking for Batch effects in PCA
batch effect pca
3.9 years ago K ▴ 50
0
votes
2
replies
1.9k
views
DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq pca pasilla
updated 6.2 years ago by ▴ 140 • written 6.2 years ago by • 0
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
0
votes
1
reply
1.6k
views
how to get tissue name of cel files?
pca oligo cel
updated 6.9 years ago by ▴ 60 • written 6.9 years ago by • 0
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
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
0
votes
1
reply
1.5k
views
Using PCA for unsupervised clustering of RNA-Seq with DESeq2
rnaseq pca deseq2 clustering
updated 7.0 years ago by 37k • written 7.0 years ago by ▴ 60
0
votes
6
replies
1.5k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
4.7 years ago lirongrossmann ▴ 60
0
votes
1
reply
1.5k
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 5.5 years ago by 37k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Query about DEXSeq
dexseq batch effect PCA
6.7 years ago n.deshpande • 0
2
votes
8
replies
1.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 3.0 years ago by 37k • written 3.0 years ago by ▴ 10
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
0
votes
7
replies
1.1k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 5.9 years ago by 37k • written 5.9 years ago by ▴ 40
0
votes
1
reply
1.0k
views
PCA analysis with 2 biological replicates
bayseq PCA
3.2 years ago bsad • 0
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
998
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
0
votes
3
replies
987
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
6.0 years ago newsomew13 • 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
1
reply
971
views
DeSeq help with PCA
deseq2 PCA
updated 6.6 years ago by 37k • written 6.6 years ago by • 0
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
2
votes
3
replies
894
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
9
votes
2
replies
881
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
0
votes
7
replies
847
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 3.7 years ago by 37k • written 3.7 years ago by • 0
0
votes
1
reply
814
views
Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
pca deseq2 rnaseq
updated 6.7 years ago by 37k • written 6.7 years ago by ▴ 190
4
votes
6
replies
807
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: ROC plot for OPLS-DA by etienne.thevenot ▴ 20
I would suggest to concatenate your training and testing data rowwise, and to apply the `opls` method with the subset parameter to select t…
Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10
Dear Basti, thank you so much! Could you please also help me how to arrange samples in the same order in rows (targests2) and columns in (…
Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k
You probably have opened that file in Excel before. Get it again directly from GEO2R, or even better take the R script GEO2R offers and run…
Comment: regression analysis for epic array methylation data using limma by Basti ▴ 280
The columns of your design matrix `var` corresponds to the coefficients that are fitted by limma. If you check your design matrix, you will…
Comment: How to figure out the FC value from Limma by beslinail • 0
I tried to FC column to dbl from chr. But FC colomn is changed by NA genlist_filter <- read_csv(file = "AD_control5.csv") gen…
Votes
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
A: Very low EdgeR Pvalues with very small sample size
A: Very low EdgeR Pvalues with very small sample size
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