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
16 days 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 7 weeks ago by 52k • written 7 weeks ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
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487
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
11 weeks ago • updated 9 weeks ago abadgerw • 0
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5
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712
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
11 weeks ago • updated 8 weeks ago abadgerw • 0
2
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9
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907
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 5 months ago by 52k • written 5 months ago by • 0
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600
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 months ago Le • 0
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4
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1.5k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
13 months ago hayleyw • 0
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1.3k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 14 months ago by 52k • written 15 months ago by • 0
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9
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1.4k
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
17 months ago hayleyw • 0
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2.2k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
22 months ago • updated 21 months ago Weiqian ▴ 10
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1.0k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
22 months ago DH • 0
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5
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1.4k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 23 months ago by 52k • written 23 months ago by • 0
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631
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.5 years ago Jonathan • 0
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.5 years ago by 52k • written 3.5 years ago by • 0
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1.6k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.6 years ago by 52k • written 3.6 years ago by ▴ 30
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1.0k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
3.8 years ago Junghoon ▴ 10
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1.4k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
3.8 years ago Junghoon ▴ 10
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1
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1.3k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
3.8 years ago • updated 3.6 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 5.3 years ago by 52k • written 5.3 years ago by ▴ 20
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8
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2.0k
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.3 years ago by ▴ 170 • written 5.4 years ago by • 0
4
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3
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2.4k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.3 years ago by ▴ 170 • written 5.6 years ago by ▴ 50
22 results • Page 1 of 1
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Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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