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pcaexplorer
•
reset
0
votes
3
replies
735
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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
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
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.
Answer: 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…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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