Showing : variancepartition • reset
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
12 weeks ago GJ • 0
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2
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
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1.2k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 0
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581
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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5
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852
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 7 months ago by 52k • written 7 months ago by • 0
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2
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694
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
11 months ago Le • 0
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4
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1.8k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
16 months ago hayleyw • 0
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1.4k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 16 months ago by 52k • written 18 months ago by • 0
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9
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
19 months ago hayleyw • 0
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5
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2.5k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.0 years ago • updated 23 months ago Weiqian ▴ 10
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.1 years ago DH • 0
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5
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1.5k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
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673
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.7 years ago Jonathan • 0
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1.7k
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
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1.7k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.8 years ago by 52k • written 3.8 years ago by ▴ 30
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1.1k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4.0 years ago Junghoon ▴ 10
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1.5k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.0 years ago Junghoon ▴ 10
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1
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1.4k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.0 years ago • updated 3.8 years ago Junghoon ▴ 10
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dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.5 years ago by ▴ 170 • written 5.6 years ago by • 0
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3
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2.6k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.5 years ago by ▴ 170 • written 5.8 years ago by ▴ 50
22 results • Page 1 of 1
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Answer: fast apply on RleList by story.benjamin ▴ 20
solved with viewApply (code is simplified below) + map reduce on chrs test.split <- split(test.gr,seqnames(test.gr)) final.st…
Comment: fast apply on RleList by story.benjamin ▴ 20
Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…
Answer: fast apply on RleList by James W. MacDonald 68k
There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…
Answer: Custom CDF creation for HTA 2.0 array using GTF annotation by James W. MacDonald 68k
It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…
Comment: how to use `arrayWeightsQuick()`? by matthew • 0
In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.
Votes
Answer: fast apply on RleList
Answer: BiocParallel_1.40.1.tar.gz not available
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
Comment: BiocParallel_1.40.1.tar.gz not available
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