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normalization
•
reset
7
votes
3
replies
15k
views
edgeR normalization method
edgeR
differential expression
normalization
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Sara
▴ 10
0
votes
4
replies
13k
views
Normalization by DEseq
Genetics
Normalization
DESeq
Genetics
Normalization
DESeq
updated 6.2 years ago by
diannedai
• 0 • written 13.5 years ago by
Rui Luo
▴ 20
2
votes
4
replies
12k
views
DESeq2 FPKM normalization
deseq2
normalization
8.2 years ago
ribioinfo
▴ 100
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
5
votes
2
replies
11k
views
lowess vs. loess
Microarray
Normalization
updated 7.9 years ago by
Gordon Smyth
50k • written 20.7 years ago by
nataraja@mit.edu
▴ 30
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
svlachavas
▴ 830
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.5 years ago
nickbern92
• 0
2
votes
1
reply
9.9k
views
How can I get the normalized read counts from TMM?
Normalization
edgeR
Normalization
edgeR
updated 11.5 years ago by
Mark Robinson
▴ 880 • written 11.5 years ago by
Reanne Bowlby
▴ 20
9
votes
11
replies
9.0k
views
Normalization using DESeq
normalization
deseq2
7.2 years ago
aangajala
▴ 20
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.8 years ago
nickp60
• 0
2
votes
4
replies
8.7k
views
pheatmap for DEGs
normalization
pheatmap
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
Hamidreza Hashemi
▴ 20
1
vote
6
replies
8.4k
views
Voom Normalization and negative numbers
Normalization
Normalization
updated 10.1 years ago by
Davis, Wade
▴ 350 • written 10.1 years ago by
Michael Breen
▴ 370
0
votes
17
replies
8.2k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 11.1 years ago by
James W. MacDonald
65k • written 11.1 years ago by
Kamila Naxerova
▴ 100
1
vote
5
replies
8.2k
views
is it possible to use TPM in DESeq2 ?
counts
Normalization
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
2
votes
4
replies
8.0k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Matan G.
▴ 60
25
votes
11
replies
7.8k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 8.4 years ago by
Simon Anders
★ 3.7k • written 8.4 years ago by
Nik Tuzov
▴ 80
1
vote
7
replies
7.6k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray
normalization
oligo HTA
updated 2.1 years ago by
Harald
• 0 • written 5.3 years ago by
RV
▴ 10
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
komal.rathi
▴ 120
2
votes
3
replies
7.2k
views
DESeq2 rlog transformation
deseq2
normalization
updated 9.4 years ago by
Wolfgang Huber
★ 13k • written 9.4 years ago by
francesca.defilippis
▴ 100
0
votes
3
replies
6.8k
views
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Microarray
Normalization
Microarray
Normalization
updated 16.1 years ago by
Wolfgang Huber
★ 13k • written 16.1 years ago by
Suprabhath Reddy Gajjala
▴ 20
9
votes
10
replies
6.8k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 13 months ago by
Chris
• 0 • written 3.5 years ago by
anikng
▴ 10
12
votes
10
replies
6.5k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.3 years ago
rached
▴ 60
1
vote
6
replies
6.3k
views
fold change calculation in edger
edger
normalization
logfc
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
tonja.r
▴ 80
1
vote
4
replies
6.2k
views
Error with Rsubread at first index: normalizePath(path.expand(path), winslash, mustWork)
normalization
4.4 years ago
peter.r.hoyt
• 0
0
votes
2
replies
6.2k
views
log transform in RMA normalization
Normalization
probe
Normalization
probe
updated 20 months ago by
snijesh
▴ 20 • written 11.3 years ago by
Jack Luo
▴ 440
1
vote
13
replies
6.1k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2
rna-seq
normalization
8.0 years ago
gil.hornung
• 0
1
vote
1
reply
5.8k
views
Voom and removing batch effect
Normalization
limma
Normalization
limma
updated 10.3 years ago by
Ryan C. Thompson
★ 7.9k • written 10.3 years ago by
Heather Estrella
▴ 30
0
votes
3
replies
5.8k
views
median normalization
Microarray
Normalization
Microarray
Normalization
updated 12.7 years ago by
James W. MacDonald
65k • written 12.7 years ago by
viritha kaza
▴ 580
1
vote
17
replies
5.6k
views
Filtering out tags with low counts in DESeq and EgdeR?
Normalization
edgeR
DESeq
Normalization
edgeR
DESeq
12.9 years ago
Xiaohui Wu
▴ 280
0
votes
5
replies
5.4k
views
How to do Affy ST array analysis
Annotation
Normalization
hgu133a
probe
affy
oligo
Annotation
Normalization
hgu133a
probe
updated 8.9 years ago by
benhrif.oussama
• 0 • written 10.0 years ago by
Guest User
★ 13k
6
votes
4
replies
5.4k
views
Method to get normalized counts in edgeR without cpm
edger
normalization
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
Pauline
▴ 20
6
votes
13
replies
5.1k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 21 months ago by
Gordon Smyth
50k • written 3.7 years ago by
harelarik
▴ 60
1
vote
3
replies
4.8k
views
EdgeR for proteomics data
Proteomics
Normalization
edgeR
Proteomics
Normalization
edgeR
updated 18 months ago by
Divya
• 0 • written 10.3 years ago by
Phinney, Brett
▴ 10
3
votes
6
replies
4.8k
views
[DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (clustering) analysis.
deseq2
normalization
variancestabilizingtransformation
updated 7.7 years ago by
minie
• 0 • written 9.0 years ago by
john
▴ 120
7
votes
12
replies
4.7k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 23 months ago by
Gordon Smyth
50k • written 8.4 years ago by
hamidrezarazzaghian
• 0
0
votes
2
replies
4.7k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Polikepahad, Sumanth
▴ 10
4
votes
1
reply
4.7k
views
norm.factors in TMM normalisation
edgr
tmm
normalization
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
4.7k
views
Normalization before ComBat
Microarray
Normalization
probe
affy
frma
Microarray
Normalization
probe
affy
frma
updated 10.5 years ago by
francesco.brundu@gmail.com
▴ 40 • written 10.5 years ago by
W. Evan Johnson
▴ 850
4
votes
6
replies
4.7k
views
How to design formula in DESeq2 when setting blind=FALSE in rlog transformation?
deseq2
normalization
9.4 years ago
Xianjun Dong
▴ 10
1
vote
2
replies
4.6k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2
normalization
microbiome
updated 9.6 years ago by
Michael Love
41k • written 9.6 years ago by
btemperton
• 0
0
votes
6
replies
4.5k
views
Question about quantile normalization and NA value
Microarray
Normalization
limma
Microarray
Normalization
limma
updated 10.3 years ago by
godahajime
▴ 20 • written 10.3 years ago by
H@mamba.fhcrc.org
▴ 10
1
vote
5
replies
4.5k
views
limma-voom
RNASeq
Normalization
limma
edgeR
RNASeq
Normalization
limma
edgeR
updated 2.1 years ago by
Gordon Smyth
50k • written 10.2 years ago by
Ming
▴ 380
4
votes
4
replies
4.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.7 years ago by
wunderl
▴ 40 • written 4.8 years ago by
neekonsu
• 0
4
votes
3
replies
4.5k
views
Differential gene expression anlaysis?
rnaseq
R
normalization
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
1234anjalianjali1234
▴ 30
1
vote
2
replies
4.4k
views
normalize count data from htseq
deseq2
normalization
9.3 years ago
Peter
• 0
0
votes
1
reply
4.4k
views
Steps of removing batch effects and hidden variables
RNASeq
Normalization
sva
RNASeq
Normalization
sva
updated 9.7 years ago by
Lucia Peixoto
▴ 330 • written 9.7 years ago by
shirley zhang
★ 1.0k
0
votes
14
replies
4.3k
views
DESeq2 count normalization
deseq2
normalization
normalized counts
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
naets_matthias
• 0
3
votes
9
replies
4.2k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray
normalization
oligo
updated 8.4 years ago by
burchard
• 0 • written 9.5 years ago by
tangboyun
▴ 30
0
votes
1
reply
4.1k
views
preprocessCore problem: normalize.quantiles error
preprocesscore
error
normalization
updated 8.8 years ago by
Diego Diez
▴ 760 • written 8.8 years ago by
gugpuccio
▴ 10
8
votes
8
replies
4.0k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq
single cell
normalization
edgeR
deseq2
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
kieranrcampbell
▴ 50
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
I don't really have any additional suggestion here.
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none
by
Michael Love
41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Votes
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
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