Showing : matrix • reset
1
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7
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6.5k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 7 weeks ago by 16k • written 5 months ago by ▴ 10
1
vote
2
replies
962
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
2.5 years ago Barista • 0
3
votes
2
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1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 2.5 years ago by • 0 • written 7.2 years ago by ★ 1.5k
3
votes
7
replies
1.4k
views
small dimensions in the matrix of counts from smallRNA using DESEq2
matrix DESeq2 SmallRNA dimensions small
2.6 years ago andreia ▴ 10
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
1
vote
2
replies
866
views
How to construct matrix and fit linear model for this microarray?
microarray dge matrix makecontrasts limma
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 10
4
votes
8
replies
1.3k
views
problem in designing matrix and batch effect
edger rna-seq matrix
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
2
votes
3
replies
1.4k
views
Filtering counts in SummarizedExperiment
diffbind matrix summarizedexperiment rangedCounts
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 60
3
votes
7
replies
3.2k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix heatmap ComplexHeatmap missing values R
updated 4.6 years ago by ▴ 260 • written 4.6 years ago by ▴ 10
2
votes
4
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1.1k
views
Are there any functions to subtract all features(rows) to a particular value(row) in the same data file?
R python normalization matrix
updated 4.7 years ago by ▴ 30 • written 4.7 years ago by ▴ 10
3
votes
1
reply
2.0k
views
Convert Flowframe to matrix
flowcore fcs flow cytommetry matrix conversion
updated 4.9 years ago by ▴ 310 • written 4.9 years ago by • 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
2
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942
views
want the piece of the matrix I wanted
matrix
updated 5.8 years ago by ★ 1.0k • written 5.8 years ago by ▴ 20
0
votes
5
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1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2 design formula matrix
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 170
3
votes
2
replies
786
views
Scoring a seq based on a matrix
matrix
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
10
votes
7
replies
2.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 60
0
votes
7
replies
2.3k
views
Deseq2 no package Matrix found
deseq2 bioconductor matrix
6.6 years ago victoria.carla.moris • 0
3
votes
8
replies
2.5k
views
S4Vectors masks/breaks regular Matrix functions
S4Vectors Matrix
7.2 years ago peter.kharchenko ▴ 30
1
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2
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1.2k
views
sva :: sva can variable of interest be a matrix itself?
sva variable of ineterest matrix
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by • 0
0
votes
1
reply
845
views
[General] compare matrix to vector higher/lower
matrix
updated 8.6 years ago by ▴ 370 • written 8.6 years ago by • 0
1
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3
replies
2.3k
views
[DiffBind] Memory issues with dba.count()
diffbind bigmemory matrix dba.count
updated 8.7 years ago by ★ 5.2k • written 8.7 years ago by ▴ 660
0
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4
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1.7k
views
reading in data and transform it to matrix format
matrix text
8.8 years ago Angel ▴ 40
22 results • Page 1 of 1
Recent ...
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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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