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plotpca
•
reset
0
votes
2
replies
329
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
4 months ago
yee
• 0
1
vote
5
replies
603
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
sara.jacobson
• 0
0
votes
3
replies
2.9k
views
How to change the dot size in plotPCA?
plotPCA
PCA
updated 12 months ago by
hediatnani
• 0 • written 13 months ago by
Yijing
• 0
2
votes
4
replies
2.3k
views
Plot PC1 and PC4 in plotPCA function
DESeq2
plotPCA
2.2 years ago • updated 2.1 years ago
synat.keam
• 0
3
votes
3
replies
6.3k
views
Adding sample label to PCA plot
plotpca
DESeq2
2.3 years ago
bjen731
▴ 10
2
votes
2
replies
1.3k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA
DESeq2
RUVSeq
removebatcheffect()
3.0 years ago
elizabethe819
• 0
1
vote
1
reply
857
views
No result from plotPCA()
DESeq2
RNASeq
plotpca
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
s1760083
• 0
0
votes
3
replies
1.0k
views
Biplot environmental variables on top of PCA
deseq2
biplot
plotpca
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
ecg1g15
▴ 20
0
votes
1
reply
633
views
Comparisons between populations
deseq2
PlotPCA
draw.triple.venn
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
N. Perera
• 0
0
votes
1
reply
594
views
PCA analysis of 2/3 samples out of a 8 sample countmatrix
deseq2
plotpca
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
snp31
• 0
12
votes
1
reply
7.1k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
lirongrossmann
▴ 80
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2
rlog
variancestabilizingtransformation
plotpca
pca
6.6 years ago
lirongrossmann
▴ 80
2
votes
4
replies
3.1k
views
DESeq2 - PCAplot differs between rlog and vsd transformation
DESeq2
plotPCA
rlog transformation
vsd
6.7 years ago
Jane Merlevede
▴ 90
14
votes
5
replies
40k
views
plotPCA - how to add labels to a PCA plot
plotPCA
deseq2
labels
updated 7.3 years ago by
Federico Marini
▴ 150 • written 7.3 years ago by
al-ash
▴ 50
0
votes
0
replies
966
views
group vectors around pca origins into 5 degrees arc cluster
pca
plotpca
7.5 years ago
marianarochadesouza
• 0
0
votes
3
replies
1.5k
views
Trouble with Custom PC Plot
deseq2
plotPCA
PCA
rna-seq
7.9 years ago
newsomew13
• 0
16 results • Page
1 of 1
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Answer: Log-cpm values from limma
by
Gordon Smyth
50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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