Showing : pcaexplorer • reset
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9
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 17 months ago by ▴ 70 • written 17 months ago by • 0
0
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4
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1.4k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 2.9 years ago by • 0
0
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3
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2.4k
views
I got error when visualizing my PCA
PCAtools pcaExplorer pcaMethods
updated 3.3 years ago by ▴ 180 • written 3.3 years ago by • 0
5
votes
6
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4.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.5 years ago Alan • 0
4
votes
7
replies
3.2k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic org.Sc.sgd.db pcaExplorer topGO EnrichmentBrowser
updated 3.7 years ago by ▴ 180 • written 3.7 years ago by • 0
9
votes
6
replies
40k
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DESeq2 / PCA Analysis of RNA-seq Data - Best Explanatory Resource?
DESeq2 pcaExplorer
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 30
2
votes
4
replies
2.5k
views
Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 3.9 years ago by ▴ 20 • written 5.2 years ago by ▴ 120
0
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7
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2.7k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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1
reply
1.6k
views
PCA on deseq2 gene data set
pcaexplorer genespca deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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8
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2.8k
views
pcaEcplorer PCA2go function crashing
pca2go pcaexplorer
updated 8.2 years ago by ▴ 180 • written 8.2 years ago by • 0
1
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2
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1.7k
views
Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of packages
deseq2 pcaexplorer
8.2 years ago reubenmcgregor88 • 0
1
vote
2
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2.0k
views
pcaExplorer error displaying PCA plot
pcaExplorer pca
updated 8.9 years ago by ▴ 180 • written 9.0 years ago by • 0
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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