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Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 10.8 years ago by ▴ 280 • written 10.8 years ago by ▴ 30
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1.7k
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
10.8 years ago noelle.noyes ▴ 30
2
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2
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1.9k
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error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
10.8 years ago noelle.noyes ▴ 30
1
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metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 10.8 years ago by ▴ 280 • written 10.8 years ago by ▴ 30
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error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 11.0 years ago by ▴ 280 • written 11.0 years ago by • 0
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DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 11.1 years ago by 43k • written 11.1 years ago by • 0
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3
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phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 11.5 years ago by ▴ 130 • written 11.5 years ago by 43k
2
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19
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3.7k
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phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 11.5 years ago by 43k • written 11.5 years ago by ▴ 130
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Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.2 years ago Luo Weijun ★ 1.6k
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Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
13.1 years ago Dan Tenenbaum ★ 8.2k
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1.8k
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Correlation analysis
Microbiome HIV Microbiome HIV
updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 20
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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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