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
1
vote
12
replies
189
views
Data normalization
DESeq2
Normalization
8 days ago • updated 6 days ago
nolwenn
• 0
0
votes
1
reply
61
views
DESEQ2 normalization for time series data
DESeq2
Normalization
Medianofratios
updated 26 days ago by
Michael Love
32k • written 26 days ago by
Joshua
• 0
3
votes
3
replies
134
views
Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
4 weeks ago • updated 29 days ago
Federico Alessandro
• 0
0
votes
3
replies
160
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 6 weeks ago by
Michael Love
32k • written 6 weeks ago by
Marina
• 0
0
votes
1
reply
75
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 6 weeks ago by
Kevin Blighe
2.7k • written 6 weeks ago by
Lara
• 0
2
votes
2
replies
97
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 8 weeks ago by
ATpoint
▴ 570 • written 8 weeks ago by
MOHAMMAD
• 0
0
votes
0
replies
81
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
11 weeks ago
wrzl
• 0
1
vote
3
replies
128
views
Normalization for two bulk RNA datasets with different library sizes
Normalization
BulkRNA-seq
DESeq2
updated 3 months ago by
Michael Love
32k • written 3 months ago by
K.
• 0
0
votes
1
reply
92
views
error using cqn package
Normalization
cqn
updated 4 months ago by
James W. MacDonald
56k • written 4 months ago by
pegah.taklifi
▴ 30
2
votes
2
replies
128
views
Normalisation in DESeq2
DESeq2
Normalization
4 months ago
Bine
▴ 10
1
vote
2
replies
172
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression
DESeq2
Normalization
updated 4 months ago by
Michael Love
32k • written 4 months ago by
krovi138
• 0
2
votes
3
replies
189
views
Normalization for within-sample gene correlation
edgeR
Normalization
DESeq2
tpm
RNASeq
updated 4 months ago by
Gordon Smyth
42k • written 4 months ago by
tcalvo
▴ 40
0
votes
2
replies
120
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData
Normalization
BatchEffect
updated 4 months ago by
Jonathan Griffiths
▴ 30 • written 4 months ago by
xyang2
▴ 120
0
votes
3
replies
494
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind
normalization
updated 5 months ago by
Rory Stark
★ 3.8k • written 4.8 years ago by
nfursova.msu
• 0
1
vote
4
replies
824
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 5 months ago by
Rory Stark
★ 3.8k • written 3.2 years ago by
ajeet
• 0
0
votes
1
reply
209
views
Normalisation of protein micro array data using VSN
microarray
normalization
protein
updated 5 months ago by
Wolfgang Huber
13k • written 22 months ago by
keniajin
• 0
0
votes
10
replies
260
views
Do I have clustering by library size?
PCA
DESeq2
Normalization
librarysize
updated 5 months ago by
Michael Love
32k • written 5 months ago by
pkachroo
▴ 10
1
vote
8
replies
336
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
5 months ago
Hesh
• 0
1
vote
1
reply
300
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 5 months ago by
Rory Stark
★ 3.8k
7
votes
8
replies
384
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 5 months ago by
Gordon Smyth
42k • written 5 months ago by
anikng
• 0
1
vote
5
replies
184
views
DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2
normalization
updated 5 months ago by
Michael Love
32k • written 5 months ago by
asrour
• 0
2
votes
7
replies
294
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger
normalization
differential exon usage
splicing
updated 6 months ago by
Yunshun Chen
▴ 720 • written 6 months ago by
oakhamwolf
• 0
1
vote
5
replies
144
views
DESeq2 library composition adjustment in size factors
deseq2
normalization
updated 6 months ago by
Michael Love
32k • written 6 months ago by
twfs
• 0
1
vote
5
replies
122
views
technical replicates and normalization/log transformation
deseq2
normalization
updated 6 months ago by
Michael Love
32k • written 6 months ago by
A
▴ 40
0
votes
2
replies
121
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 7 months ago by
Kevin Blighe
2.7k • written 7 months ago by
linouhao
• 0
1
vote
2
replies
99
views
tcga and geo train and validation sets
deseq2
normalization
updated 7 months ago by
Michael Love
32k • written 7 months ago by
linouhao
• 0
0
votes
2
replies
117
views
How to normalise data in ballgown?
r
normalization
edger
updated 7 months ago by
James W. MacDonald
56k • written 7 months ago by
lakshmi9c
• 0
2
votes
4
replies
146
views
Deseq2's geometric mean calculation and 0s
deseq2
normalization
updated 7 months ago by
Michael Love
32k • written 7 months ago by
lmrogers34
• 0
6
votes
13
replies
476
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 7 months ago by
Gordon Smyth
42k • written 7 months ago by
harelarik
▴ 50
2
votes
3
replies
144
views
Differential gene expression using Ballgown
r
normalization
7 months ago
lakshmi9c
• 0
1
vote
2
replies
100
views
Unexpected rlog values when count spread is large
deseq2
normalization
updated 8 months ago by
Michael Love
32k • written 8 months ago by
eric.blanc
• 0
2
votes
8
replies
293
views
Differential gene expression using R
deseq2
edger
normalization
limma
updated 8 months ago by
Gordon Smyth
42k • written 8 months ago by
lakshmi9c
• 0
2
votes
4
replies
705
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 8 months ago by
Kevin Blighe
2.7k • written 8 months ago by
Matan G.
▴ 30
2
votes
2
replies
104
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger
normalization
updated 8 months ago by
James W. MacDonald
56k • written 8 months ago by
ahmedaalkarim
• 0
0
votes
1
reply
84
views
Input of tscR
microarray
normalization
tscR
time-course
updated 8 months ago by
Kevin Blighe
2.7k • written 8 months ago by
keremwai
• 0
0
votes
0
replies
107
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq
normalization
GC
length
RNASeq
8 months ago
abf
▴ 30
0
votes
2
replies
111
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind
MA plot
normalization
ChIP-seq
updated 8 months ago by
Rory Stark
★ 3.8k • written 8 months ago by
hasse.bossenbroek
• 0
2
votes
6
replies
255
views
Question: Method to get normalize allele specific read counts
edger
normalization
updated 9 months ago by
Aaron Lun
★ 26k • written 9 months ago by
hemantcnaik
• 0
0
votes
0
replies
58
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN
normalization
9 months ago
tofukaj
• 0
7
votes
10
replies
197
views
is there a function in edger the same as vst or rlog in deseq2
edger
normalization
deseq2
updated 10 months ago by
Gordon Smyth
42k • written 10 months ago by
linouhao
• 0
2
votes
1
reply
150
views
Cross-species analysis and normalization with DESeq2
normalization
deseq2
across species
rnaseq
updated 10 months ago by
Michael Love
32k • written 10 months ago by
rmurray2050
• 0
4
votes
10
replies
187
views
how to analyze WGCNA results?
cancer
probe
deseq2
annotation
normalization
updated 11 months ago by
Kevin Blighe
2.7k • written 11 months ago by
rajpal22288
▴ 10
0
votes
1
reply
132
views
DESeq2 and Heatmap for multiple conditions
deseq2
normalization
updated 11 months ago by
Michael Love
32k • written 11 months ago by
Hamidreza Hashemi
▴ 20
2
votes
7
replies
222
views
ControlGenes/ housekeeping genes Deseq2
normalization
deseq2
sizefactors
updated 11 months ago by
Michael Love
32k • written 11 months ago by
mankadeep2
▴ 20
4
votes
3
replies
987
views
How to plot the batch corrected values in DESeq2
deseq2
normalization
updated 11 months ago by
Michael Love
32k • written 2.3 years ago by
dhwani.dholakia
• 0
1
vote
4
replies
632
views
pheatmap for DEGs
normalization
pheatmap
updated 11 months ago by
Kevin Blighe
2.7k • written 11 months ago by
Hamidreza Hashemi
▴ 20
0
votes
2
replies
170
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2
edgeR
repenrich2
normalization
11 months ago
mkmwong
• 0
0
votes
3
replies
70
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2
normalization
updated 12 months ago by
Michael Love
32k • written 12 months ago by
jillian.waters
• 0
0
votes
2
replies
79
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2
normalization
updated 12 months ago by
Bob Thurman
• 0 • written 12 months ago by
ericmalekos
• 0
0
votes
3
replies
87
views
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
normalization
updated 12 months ago by
Gordon Smyth
42k • written 12 months ago by
shenjun_renji
• 0
1,643 results • Page
1 of 33
Recent ...
Replies
Answer: DepMap copy number
by
Laurent Gatto
1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp
by
James W. MacDonald
56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq
by
Naomi Altman
★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile
by
Mike Smith
★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db
by
Xulei Huo
• 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
Awards
• All
Scholar
to
James W. MacDonald
56k
Popular Question
to
Assa Yeroslaviz
★ 1.5k
Teacher
to
Martin Morgan
25k
Scholar
to
Michael Love
32k
Teacher
to
Naomi Altman
★ 6.0k
Locations
• All
European Union,
6 minutes ago
Austria,
9 minutes ago
United States,
20 minutes ago
United States,
39 minutes ago
Belgium,
40 minutes ago
Traffic: 454 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