Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
normalization
•
reset
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 9 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 5 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
2
votes
1
reply
320
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 7 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
2
votes
2
replies
712
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
4 months ago
Linton
• 0
2
votes
3
replies
388
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
4
replies
649
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
2
votes
2
replies
438
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
3 months ago
jackafiore
• 0
2
votes
2
replies
417
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
1
vote
1
reply
451
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 4 months ago by
Michael Love
42k • written 4 months ago by
phmai1148
• 0
1
vote
6
replies
459
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
RL
• 0
1
vote
5
replies
1.1k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI
normalization
limma
voom
Normalization
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 18 months ago by
Sarah
• 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
1
vote
3
replies
626
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 3 months ago by
georgii.vdovin
• 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 9 months ago by
Gordon Smyth
50k • written 3.7 years ago by
linouhao
▴ 20
1
vote
4
replies
313
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 weeks ago
samuel.channon
• 0
0
votes
1
reply
106
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization
edgeR
Normalization
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 10.3 years ago by
Guest User
★ 13k
0
votes
0
replies
300
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
7 months ago
Florian
• 0
0
votes
0
replies
267
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
6 months ago
vasily.dobrovolsky
• 0
0
votes
1
reply
333
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Ömür Koray
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 8 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
6
replies
920
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
3
replies
620
views
Normalization of different input materials
Normalization
DESeq2
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
altuda
▴ 10
0
votes
2
replies
780
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
11 months ago
dwas
• 0
0
votes
1
reply
91
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 4 days ago by
Michael Love
42k • written 5 days ago by
piemmea
• 0
0
votes
0
replies
168
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
10 weeks ago • updated 8 weeks ago
Giovanni Calice
▴ 160
0
votes
2
replies
197
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
6 weeks ago
Marianna
▴ 20
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 6 months ago by
Gordon Smyth
50k • written 12.5 years ago by
Guest User
★ 13k
33 results • Page
1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Locations
• All
Russia,
28 minutes ago
Poland,
35 minutes ago
Hong Kong,
36 minutes ago
South Korea,
53 minutes ago
The city by the bay,
1 hour ago
Traffic: 435 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6