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Showing :
Normalization
•
reset
0
votes
0
replies
86
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
14 days ago • updated 4 hours ago
Giovanni Calice
▴ 160
2
votes
1
reply
228
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 3.9k • written 4 weeks ago by
Shaimaa Gamal
• 0
2
votes
2
replies
259
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
5 weeks ago
jackafiore
• 0
2
votes
3
replies
276
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
461
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 7 weeks ago by
georgii.vdovin
• 0
0
votes
1
reply
189
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 7 weeks ago by
ATpoint
★ 3.9k • written 7 weeks ago by
Ömür Koray
• 0
2
votes
4
replies
426
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
8 weeks ago
Sabiha
▴ 20
1
vote
1
reply
329
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 10 weeks ago by
Michael Love
41k • written 10 weeks ago by
phmai1148
• 0
2
votes
2
replies
409
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
10 weeks ago
Linton
• 0
0
votes
0
replies
204
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
4 months ago
vasily.dobrovolsky
• 0
0
votes
6
replies
693
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
4 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
228
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
1
vote
11
replies
830
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
cm15245
• 0
1
vote
4
replies
2.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 16 months ago by
Sarah
• 0
1
vote
5
replies
922
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 8 months ago by
Gordon Smyth
50k • written 8 months ago by
manuelsokolov
• 0
0
votes
3
replies
546
views
Normalization of different input materials
Normalization
DESeq2
updated 8 months ago by
ATpoint
★ 3.9k • written 8 months ago by
altuda
▴ 10
0
votes
2
replies
675
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
9 months ago
dwas
• 0
5
votes
11
replies
2.6k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 9 months ago by
Sabiha
▴ 20
0
votes
3
replies
644
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
FedeXander
• 0
1
vote
2
replies
801
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
11 months ago
Abdul
▴ 20
2
votes
2
replies
599
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
11 months ago
Abdul
▴ 20
1
vote
2
replies
562
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 11 months ago by
Sarah
• 0
0
votes
2
replies
623
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
11 months ago
Assa Yeroslaviz
★ 1.5k
1
vote
6
replies
1.6k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 7 months ago by
Gordon Smyth
50k • written 3.5 years ago by
linouhao
▴ 20
2
votes
3
replies
1.6k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 11 months ago by
ATpoint
★ 3.9k • written 12 months ago by
SH
• 0
1
vote
1
reply
867
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
SH
• 0
0
votes
1
reply
500
views
Using DESeq2 only for normalization
DESeq2
Normalization
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
phmai1148
• 0
0
votes
1
reply
369
views
processing samples with significantly different counts
DESeq2
Normalization
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
Anastasiia
• 0
0
votes
5
replies
1.1k
views
DESeq Normalization and miRNAs Filtering
DESeq2
Normalization
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
phmai1148
• 0
2
votes
3
replies
798
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
suphamon.j
▴ 20
0
votes
1
reply
485
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
marslena
• 0
3
votes
3
replies
747
views
What is cpmByGroup used for?
edgeR
Normalization
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
EM
• 0
0
votes
2
replies
668
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent
StatisticalMethod
edgeR
MultidimensionalScaling
Normalization
13 months ago
rcreswell01
• 0
1
vote
1
reply
672
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
tleona3
• 0
4
votes
2
replies
1.5k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 13 months ago by
ATpoint
★ 3.9k • written 13 months ago by
kalavattam
▴ 10
0
votes
1
reply
569
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Aleksandra
• 0
0
votes
1
reply
1.2k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 14 months ago by
Michael Love
41k • written 14 months ago by
kalavattam
▴ 10
4
votes
7
replies
1.8k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
14 months ago • updated 13 months ago
Bernardo
▴ 10
1
vote
0
replies
520
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
14 months ago
Arend
▴ 10
0
votes
0
replies
641
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
14 months ago
Zhijie
• 0
1
vote
0
replies
575
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
14 months ago
r_grau
▴ 10
3
votes
4
replies
1.5k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
15 months ago • updated 14 months ago
spg
• 0
4
votes
8
replies
2.0k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 9 months ago by
Gordon Smyth
50k • written 15 months ago by
Sabiha
▴ 20
0
votes
1
reply
585
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 15 months ago by
ATpoint
★ 3.9k • written 15 months ago by
Deniz
• 0
0
votes
2
replies
917
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 15 months ago by
ATpoint
★ 3.9k • written 15 months ago by
lola
• 0
2
votes
4
replies
3.2k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
15 months ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
845
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
wiscoyogi
• 0
0
votes
2
replies
718
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization
R
cqn
16 months ago
Sally
• 0
1
vote
2
replies
770
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
16 months ago
mohammedtoufiq91
▴ 10
3
votes
6
replies
1.8k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
16 months ago
Sara
• 0
50 results • Page
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Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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