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RNASEQ
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Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
just now
james.zhang20
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 19 hours ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
122
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
0
votes
1
reply
129
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
taur.vil
• 0
0
votes
2
replies
192
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RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
12 days ago • updated 9 days ago
catv
• 0
3
votes
1
reply
155
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
99
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 13 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
0
votes
1
reply
131
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Merav
• 0
1
vote
3
replies
843
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 7 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
2
replies
904
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 14 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
5
replies
1.8k
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EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
11 results • Page
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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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