Showing : PCa • reset
5
votes
7
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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
4
votes
5
replies
6.6k
views
outlier detection of RNAseq samples
deseq2 rnaseq PCA hierarchical clustering outlier
7.4 years ago wd ▴ 30
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
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
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
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
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
9
votes
2
replies
1.7k
views
Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 6.6 years ago by ▴ 110 • written 6.6 years ago by ★ 7.9k
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
0
votes
3
replies
1.5k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
8.0 years ago newsomew13 • 0
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
1
vote
2
replies
1.8k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
6.0 years ago JoannaF ▴ 10
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
1
vote
2
replies
989
views
nice 3D displays for PCA analysis
PCA
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 670
0
votes
3
replies
2.0k
views
Query about DEXSeq
dexseq batch effect PCA
8.7 years ago n.deshpande • 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
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
4
votes
1
reply
3.7k
views
PCA plot on DE genes do not separate samples. DESeq2.
deseq2 pca
updated 8.1 years ago by 65k • written 8.1 years ago by ▴ 10
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
3
votes
2
replies
1.7k
views
How to find genes causing the high variance of one replicate in the PCA
pca variance deseq2 gene_id
updated 7.9 years ago by 42k • written 7.9 years ago by ▴ 10
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 7.9 years ago by ★ 7.9k • written 7.9 years ago by • 0
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
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
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
2
votes
1
reply
2.8k
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 7.5 years ago by 42k • written 7.5 years ago by ▴ 20
1
vote
2
replies
1.5k
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 7.5 years ago by ▴ 150 • written 7.5 years ago by • 0
2
votes
2
replies
1.1k
views
pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 10
0
votes
1
reply
1.1k
views
pca plot for tissues and protein values
pca
updated 6.9 years ago by 65k • written 6.9 years ago by ▴ 40
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
12
votes
1
reply
7.2k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.5 years ago by 42k • written 6.6 years ago by ▴ 80
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.5 years ago by ▴ 20
1
vote
3
replies
4.5k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
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
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
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
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
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
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
4
votes
2
replies
3.4k
views
PCA for voom normalized RNAseq data
voom pca
updated 9.1 years ago by ★ 28k • written 9.1 years ago by ▴ 120
0
votes
1
reply
1.9k
views
Using PCA for unsupervised clustering of RNA-Seq with DESeq2
rnaseq pca deseq2 clustering
updated 9.0 years ago by 42k • written 9.0 years ago by ▴ 60
2
votes
1
reply
2.1k
views
biplot diagram of PCA analysis differs from plot of variables
r pca biplot
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
votes
1
reply
2.0k
views
how to get tissue name of cel files?
pca oligo cel
updated 8.9 years ago by ▴ 60 • written 8.9 years ago by • 0
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
0
votes
1
reply
1.1k
views
Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
pca deseq2 rnaseq
updated 8.7 years ago by 42k • written 8.7 years ago by ▴ 250
1
vote
1
reply
1.3k
views
DeSeq help with PCA
deseq2 PCA
updated 8.5 years ago by 42k • written 8.5 years ago by • 0
2
votes
1
reply
3.3k
views
PCA from deseq and r function differ
deseq2 pca
updated 8.5 years ago by 42k • written 8.5 years ago by ▴ 80
6
votes
1
reply
14k
views
Deseq2 PCA plot customize
deseq2 pca
updated 8.3 years ago by 42k • written 8.3 years ago by ▴ 40
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
3
votes
1
reply
2.0k
views
does pca assume no heteroscedasticity?
deseq2 pca
updated 8.3 years ago by 42k • written 8.3 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
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.
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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