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PlotPCA
•
reset
0
votes
2
replies
1.3k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
2.0 years ago
yee
• 0
1
vote
5
replies
1.6k
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
sara.jacobson
• 0
0
votes
3
replies
6.2k
views
How to change the dot size in plotPCA?
plotPCA
PCA
updated 2.7 years ago by
hediatnani
• 0 • written 2.7 years ago by
Yijing
• 0
3
votes
5
replies
3.6k
views
Plot PC1 and PC4 in plotPCA function
DESeq2
plotPCA
updated 18 months ago by
Daniele
• 0 • written 3.9 years ago by
synat.keam
• 0
3
votes
3
replies
10k
views
Adding sample label to PCA plot
plotpca
DESeq2
3.9 years ago
bjen731
▴ 10
2
votes
2
replies
2.1k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
4.6 years ago
elizabethe819
• 0
1
vote
1
reply
1.4k
views
No result from plotPCA()
DESeq2
RNASeq
plotpca
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
s1760083
• 0
0
votes
3
replies
1.6k
views
Biplot environmental variables on top of PCA
deseq2
biplot
plotpca
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
ecg1g15
▴ 30
0
votes
1
reply
949
views
Comparisons between populations
deseq2
PlotPCA
draw.triple.venn
updated 7.2 years ago by
Michael Love
43k • written 7.3 years ago by
N. Perera
• 0
0
votes
1
reply
975
views
PCA analysis of 2/3 samples out of a 8 sample countmatrix
deseq2
plotpca
updated 7.2 years ago by
Michael Love
43k • written 7.3 years ago by
snp31
• 0
12
votes
1
reply
8.4k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 8.1 years ago by
Michael Love
43k • written 8.1 years ago by
lirongrossmann
▴ 80
0
votes
6
replies
4.2k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
8.2 years ago
lirongrossmann
▴ 80
2
votes
4
replies
3.8k
views
DESeq2 - PCAplot differs between rlog and vsd transformation
DESeq2
plotPCA
rlog transformation
vsd
8.4 years ago
Jane Merlevede
▴ 90
14
votes
5
replies
50k
views
plotPCA - how to add labels to a PCA plot
plotPCA
deseq2
labels
updated 8.9 years ago by
Federico Marini
▴ 180 • written 8.9 years ago by
al-ash
▴ 50
0
votes
0
replies
1.3k
views
group vectors around pca origins into 5 degrees arc cluster
pca
plotpca
9.2 years ago
marianarochadesouza
• 0
0
votes
3
replies
2.0k
views
Trouble with Custom PC Plot
deseq2
plotPCA
PCA
rna-seq
9.6 years ago
newsomew13
• 0
16 results • Page
1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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