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156 results • Page
3 of 4
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Votes
Replies
0
votes
1
reply
812
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 1 day ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 4 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 1 day ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
0
replies
728
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 2 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 4 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 4 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 4 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 2 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 2 days ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
1
vote
1
reply
653
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 2 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 2 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 2 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 2 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 2 days ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
0
votes
1
reply
826
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 2 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 2 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 2 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 2 days ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
0
replies
665
views
Conditions for valid batch effect correction
r
batch-effect
updated 2 days ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 2 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 1 day ago by
Ram
43k • written 5.4 years ago by
baldissera152
▴ 10
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 2 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
0
replies
835
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 2 days ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
RC
▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 2 days ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 2 days ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 2 days ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
0
replies
1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq
gene-expression-matrix
correlation
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
aiswaryabioinfo
▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 1 day ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 2 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 1 day ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 6.7 years ago by
Dipro
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 2 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 1 day ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 1 day ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 1 day ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 1 day ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 1 day ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 2 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 7.1 years ago by
German.M.Demidov
★ 2.9k
0
votes
0
replies
1.7k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 2 days ago by
Ram
43k • written 7.1 years ago by
vakul.mohanty
▴ 270
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 1 day ago by
Ram
43k • written 7.4 years ago by
oselm
▴ 50
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Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
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