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dream
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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
8 months ago
hayleyw
• 0
1
vote
4
replies
682
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
13 months ago
DH
• 0
0
votes
5
replies
951
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Le
• 0
8
votes
11
replies
2.4k
views
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 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
hermidalc
▴ 20
4
votes
3
replies
1.7k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 4.6 years ago by
gabriel.hoffman
▴ 110 • written 4.8 years ago by
Ben
▴ 50
5 results • Page
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Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
James W. MacDonald
65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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