Showing : heatmap.2 • reset
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Add 'ColSideColors' using 'heatmap.2' function
ColSideColors heatmaps heatmap.2
updated 5 months ago by ▴ 80 • written 6 months ago by ▴ 10
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505
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collided row names in heatmap.2
heatmap.2 genefilter deseq2
updated 2.1 years ago by 63k • written 2.1 years ago by • 0
2
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2
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3.4k
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ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 5.1 years ago by 63k • written 5.1 years ago by • 0
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1
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650
views
RPKM representation in heatmap is not accurate
heatmap.2 z-score
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
5
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3
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10k
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Interpreting heatmap in DESEQ2
deseq2 heatmap.2
updated 5.5 years ago by ▴ 150 • written 5.5 years ago by • 0
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0
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1.4k
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Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
5.6 years ago lawarde.ankita1 ▴ 30
4
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8
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7.4k
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Scaling genes to have unit variance for clustering / heatmaps with DESeq2
deseq2 heatmap.2 bicluster pheatmap
updated 5.9 years ago by 40k • written 8.1 years ago by ▴ 10
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2
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966
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gene names disapper from heatmap.2 after adding gene descripton
heatmap.2 edger
6.0 years ago mictadlo ▴ 10
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4
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5.9k
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Sample-to-sample distance matrix using heatmap.2
heatmap.2 gplots DESeq2
6.0 years ago Jane Merlevede ▴ 90
8
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1
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8.6k
views
extracting the genes associated with the clusters
heatmap.2 pheatmap complexheatmap heatplus
updated 6.6 years ago by ▴ 670 • written 6.6 years ago by ▴ 660
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1
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1.5k
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heatmap.2 reorder branches
heatmap.2 hclust reorderfun
updated 6.6 years ago by 63k • written 6.6 years ago by ▴ 360
2
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1
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3.0k
views
Assign custom dendrogram to ComplexHeatmap Heatmap object
complexheatmap heatmap.2 dendrogram dendextend heatmap
updated 6.9 years ago by ▴ 200 • written 6.9 years ago by ▴ 660
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3
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1.9k
views
How to combine replicates creating heatmap?
deseq2 edgeR heatmap.2
updated 6.9 years ago by 40k • written 6.9 years ago by ▴ 40
1
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5
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3.7k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2 heatmap edgeR deseq2 deseq
updated 7.4 years ago by 40k • written 7.4 years ago by ▴ 10
1
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1
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1.4k
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heatmap2 error key
heatmap.2
updated 7.4 years ago by 63k • written 7.4 years ago by ▴ 80
1
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2
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2.3k
views
R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
pheatmap heatmap.2
7.5 years ago John ▴ 30
1
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0
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2.4k
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heatmap.2() making columns narrower to make them look like microarray?
heatmap.2 pheatmap
8.0 years ago AJC ▴ 10
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0
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2.4k
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Problem with the colors in the heatmap.2 function and the color key values range
gplots heatmap.2 affymetrix microarrays color key
8.1 years ago svlachavas ▴ 810
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2
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9.7k
views
Use of various distance measures and clustering methods in heatmap creation
gplots heatmap.2 bioconductor pearsoncorrelation average
8.2 years ago svlachavas ▴ 810
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2
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1.2k
views
Possible construction of heatmap for clustering only genes for different treatments and not samples
heatmap.2 clustering common DEG genes bioconductor
updated 8.2 years ago by 63k • written 8.3 years ago by ▴ 810
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1
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1.3k
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Error when trying to plot sample distance from and assay object generated with DESeq2
deseq2 heatmap.2
updated 8.3 years ago by 40k • written 8.3 years ago by ▴ 30
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7
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4.5k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
8.5 years ago svlachavas ▴ 810
22 results • Page 1 of 1
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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