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timecourse
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6
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.5 years ago by
Camila Orellana
▴ 10
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2
timecourse
design and contrast matrix
updated 7 weeks ago by
ta_awwad
▴ 10 • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
smac97
• 0
1
vote
6
replies
909
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Debebe
• 0
0
votes
1
reply
559
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Fred
• 0
0
votes
1
reply
506
views
DESeq2, Timecourse using fitted splines
timecoursedata
RNASeqData
TimeCourse
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
georgii.vdovin
• 0
0
votes
1
reply
265
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
0
votes
1
reply
241
views
Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2
timecourse
time
updated 3 months ago by
Michael Love
41k • written 3 months ago by
Anastasiia
• 0
0
votes
2
replies
154
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
joshua.mannheimer
• 0
9 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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