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Showing :
pcaExplorer
•
reset
0
votes
3
replies
735
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 17 months ago by
James
• 0
0
votes
3
replies
1.1k
views
I got error when visualizing my PCA
PCAtools
pcaExplorer
pcaMethods
updated 22 months ago by
Federico Marini
▴ 150 • written 22 months ago by
m610110001
• 0
5
votes
6
replies
2.4k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.0 years ago
Alan
• 0
4
votes
7
replies
1.9k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic
org.Sc.sgd.db
pcaExplorer
topGO
EnrichmentBrowser
updated 2.2 years ago by
Federico Marini
▴ 150 • written 2.2 years ago by
chase.mateusiak
• 0
2
votes
4
replies
1.5k
views
Comparing discrete variable to PCA
EDA
pcaExplorer
PCAtools
PCA
updated 2.4 years ago by
Miguel
▴ 10 • written 3.7 years ago by
k.vitting.seerup
▴ 120
9
votes
6
replies
27k
views
DESeq2 / PCA Analysis of RNA-seq Data - Best Explanatory Resource?
DESeq2
pcaExplorer
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
vanbelj
▴ 30
0
votes
7
replies
1.8k
views
go_bp table in custom OrgDb package
annotation
go
pcaExplorer
AnnotationForge
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
psutton
• 0
0
votes
1
reply
1.1k
views
PCA on deseq2 gene data set
pcaexplorer
genespca
deseq2
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
sally_b86
• 0
0
votes
8
replies
2.1k
views
pcaEcplorer PCA2go function crashing
pca2go
pcaexplorer
updated 6.7 years ago by
Federico Marini
▴ 150 • written 6.7 years ago by
reubenmcgregor88
• 0
1
vote
2
replies
1.3k
views
Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of packages
deseq2
pcaexplorer
6.7 years ago
reubenmcgregor88
• 0
1
vote
2
replies
1.5k
views
pcaExplorer error displaying PCA plot
pcaExplorer
pca
updated 7.4 years ago by
Federico Marini
▴ 150 • written 7.4 years ago by
swaegers.janne
• 0
11 results • Page
1 of 1
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Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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