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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
1
vote
6
replies
910
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
3
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5
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1.3k
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DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 9 months ago by
Michael Love
41k • written 10 months ago by
smac97
• 0
0
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2
replies
1.4k
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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
0
votes
2
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155
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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
0
votes
1
reply
559
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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
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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
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1
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241
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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
1
reply
265
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DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
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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