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Showing :
Normalization
•
reset
1
vote
12
replies
134
views
Data normalization
DESeq2
Normalization
2 days ago • updated 1 day ago
nolwenn
• 0
0
votes
1
reply
58
views
DESEQ2 normalization for time series data
DESeq2
Normalization
Medianofratios
updated 21 days ago by
Michael Love
32k • written 21 days ago by
Joshua
• 0
3
votes
3
replies
130
views
Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
28 days ago • updated 24 days ago
Federico Alessandro
• 0
0
votes
3
replies
156
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 5 weeks ago by
Michael Love
32k • written 5 weeks ago by
Marina
• 0
0
votes
1
reply
73
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 5 weeks ago by
Kevin Blighe
2.7k • written 5 weeks ago by
Lara
• 0
2
votes
2
replies
97
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 7 weeks ago by
ATpoint
▴ 570 • written 8 weeks ago by
MOHAMMAD
• 0
0
votes
0
replies
78
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
10 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 12 weeks ago by
Michael Love
32k • written 12 weeks ago by
K.
• 0
0
votes
1
reply
90
views
error using cqn package
Normalization
cqn
updated 3 months ago by
James W. MacDonald
56k • written 3 months ago by
pegah.taklifi
▴ 30
2
votes
2
replies
127
views
Normalisation in DESeq2
DESeq2
Normalization
4 months ago
Bine
▴ 10
1
vote
2
replies
171
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
186
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
118
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
491
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
822
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
207
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
257
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
332
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
5 months ago
Hesh
• 0
1
vote
1
reply
296
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
376
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
180
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
286
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger
normalization
differential exon usage
splicing
updated 5 months ago by
Yunshun Chen
▴ 720 • written 5 months ago by
oakhamwolf
• 0
1
vote
5
replies
138
views
DESeq2 library composition adjustment in size factors
deseq2
normalization
updated 5 months ago by
Michael Love
32k • written 6 months ago by
twfs
• 0
1
vote
5
replies
120
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
119
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 6 months ago by
Kevin Blighe
2.7k • written 6 months ago by
linouhao
• 0
1
vote
2
replies
98
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
115
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
143
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
467
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
141
views
Differential gene expression using Ballgown
r
normalization
7 months ago
lakshmi9c
• 0
1
vote
2
replies
97
views
Unexpected rlog values when count spread is large
deseq2
normalization
updated 7 months ago by
Michael Love
32k • written 7 months ago by
eric.blanc
• 0
2
votes
8
replies
287
views
Differential gene expression using R
deseq2
edger
normalization
limma
updated 7 months ago by
Gordon Smyth
42k • written 7 months ago by
lakshmi9c
• 0
2
votes
4
replies
695
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
100
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
80
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
105
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
108
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
252
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
55
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
194
views
is there a function in edger the same as vst or rlog in deseq2
edger
normalization
deseq2
updated 9 months ago by
Gordon Smyth
42k • written 9 months ago by
linouhao
• 0
2
votes
1
reply
149
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
185
views
how to analyze WGCNA results?
cancer
probe
deseq2
annotation
normalization
updated 10 months ago by
Kevin Blighe
2.7k • written 10 months ago by
rajpal22288
▴ 10
0
votes
1
reply
126
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
207
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
981
views
How to plot the batch corrected values in DESeq2
deseq2
normalization
updated 11 months ago by
Michael Love
32k • written 2.2 years ago by
dhwani.dholakia
• 0
1
vote
4
replies
621
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
167
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2
edgeR
repenrich2
normalization
11 months ago
mkmwong
• 0
0
votes
3
replies
67
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2
normalization
updated 11 months ago by
Michael Love
32k • written 11 months ago by
jillian.waters
• 0
0
votes
2
replies
77
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2
normalization
updated 11 months ago by
Bob Thurman
• 0 • written 11 months ago by
ericmalekos
• 0
0
votes
3
replies
84
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
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Recent ...
Replies
Answer: Differential Transcript Usage: complex factorial design
by
Gordon Smyth
42k
edgeR does differential expression for transcripts via the catchSalmon function followed the usual edgeR pipelines as you would do for gene…
Comment: RSamtools idxstatsBam not working with remote bam file
by
mja18
▴ 30
Thanks Martin. Yes, that works.
Answer: RSamtools idxstatsBam not working with remote bam file
by
Martin Morgan
25k
Can you tell me if the following works for you? In a new R session ```{r} library(Rsamtools) setMethod(idxstatsBam, "BamFile", …
Comment: Aspli: error with gbCounts
by
achernomoretz
• 0
Hi Jeremy. We got it and we are working on the issue. Thanks for your patience. A
Comment: Aspli: error with gbCounts
by
jbono
• 0
Sorry, I forgot to respond here that I sent the file via email. Please let me know if you didn't receive it, thanks!
Votes
Answer: RSamtools idxstatsBam not working with remote bam file
Running > 100 samples per group - memory issues
R failing to load genome files from EnsDb.Hsapiens.v86
Comment: TCGA data analysis
Comment: BSGenome Forge for non-model organism
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