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PrincipalComponent
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Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 17 months ago by
James
• 0
0
votes
2
replies
740
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent
StatisticalMethod
edgeR
MultidimensionalScaling
Normalization
14 months ago
rcreswell01
• 0
0
votes
2
replies
308
views
PCA after DESeq2
DESeq2
PrincipalComponent
prin
DifferentialExpression
updated 3 months ago by
Michael Love
42k • written 3 months ago by
Shaimaa Gamal
• 0
1
vote
1
reply
844
views
PCA rand heatmap of raw data
DESeq2
DiffSeq
PrincipalComponent
rlog
heatmaps
updated 3.2 years ago by
Michael Love
42k • written 3.2 years ago by
Fischer-philipp
▴ 30
0
votes
1
reply
901
views
DiffBind: dba.plotPCA() ellipse
PrincipalComponent
DiffBind
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
Lisa
• 0
0
votes
1
reply
440
views
How to extract proteins from PCs in plot_pca in DEP package
DEP
PrincipalComponent
PCA
plot_pca
updated 13 months ago by
Basti
▴ 780 • written 13 months ago by
fuqichen1
• 0
6 results • Page
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Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Votes
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
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
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