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RNA-SEQ
•
reset
0
votes
2
replies
270
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
4 months ago
davca
• 0
0
votes
4
replies
622
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
5 months ago
ar14g12
• 0
2
votes
3
replies
1.3k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
gingergeiger22
• 0
0
votes
3
replies
604
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 6 months ago by
Alejandro Reyes
★ 1.9k • written 7 months ago by
Alice
• 0
3
votes
4
replies
799
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
7 months ago
Eva
▴ 10
0
votes
3
replies
619
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 9 months ago by
Michael Love
41k • written 9 months ago by
samuelcjx
• 0
5
votes
7
replies
1.1k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
659
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
FedeXander
• 0
0
votes
3
replies
800
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
FedeXander
• 0
1
vote
1
reply
1.2k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
SH
• 0
0
votes
2
replies
2.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 7 months ago by
manuel.fernandez
• 0 • written 23 months ago by
cicely.day
• 0
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 10 months ago by
Rob
• 0 • written 3.4 years ago by
microPhD
• 0
0
votes
2
replies
3.4k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.7 years ago by
ag1805x
▴ 80
0
votes
10
replies
2.1k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.0 years ago by
saddamhusain77
• 0
0
votes
1
reply
864
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 3 months ago by
ATpoint
★ 4.0k • written 5.9 years ago by
saad_k6
• 0
15 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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