Showing : normalization • reset
2
votes
3
replies
75
views
vst of DESeq2 for bulk UMI counts
DESeq2 normaliz Normalization
updated 5 days ago by 33k • written 5 days ago by • 0
0
votes
1
reply
90
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 8 days ago by ▴ 60 • written 16 days ago by • 0
0
votes
1
reply
149
views
DESseq2 question about VST and rlog
DESeq2 Normalization
updated 26 days ago by ▴ 700 • written 26 days ago by • 0
1
vote
0
replies
92
views
Normalization of metabolomics/lipidomics data for limma
Lipidomics Metabolomics limma Normalization
27 days ago pgugger ▴ 60
0
votes
1
reply
95
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 29 days ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
5
replies
233
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 6 weeks ago by 33k • written 8 weeks ago by • 0
1
vote
1
reply
136
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 8 weeks ago by ▴ 890 • written 8 weeks ago by ▴ 10
2
votes
2
replies
125
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
10 weeks ago geoffrey ▴ 10
0
votes
4
replies
205
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
12 weeks ago Yuqia • 0
0
votes
0
replies
90
views
Cross-cultivar RNA-seq analysis
RNA Normalization
3 months ago nancy • 0
1
vote
12
replies
369
views
Data normalization
DESeq2 Normalization
3 months ago nolwenn • 0
0
votes
1
reply
129
views
DESEQ2 normalization for time series data
DESeq2 Normalization Medianofratios
updated 4 months ago by 33k • written 4 months ago by • 0
3
votes
3
replies
239
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4 months ago Federico Alessandro • 0
0
votes
3
replies
273
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 4 months ago by 33k • written 5 months ago by • 0
0
votes
1
reply
142
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 4 months ago by 3.2k • written 5 months ago by • 0
2
votes
2
replies
186
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 5 months ago by ▴ 700 • written 5 months ago by • 0
0
votes
0
replies
137
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
6 months ago wrzl • 0
1
vote
3
replies
196
views
Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 6 months ago by 33k • written 6 months ago by • 0
0
votes
1
reply
143
views
error using cqn package
Normalization cqn
updated 7 months ago by 57k • written 7 months ago by ▴ 30
2
votes
2
replies
181
views
Normalisation in DESeq2
DESeq2 Normalization
8 months ago • updated 7 months ago Bine ▴ 10
1
vote
2
replies
243
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 8 months ago by 33k • written 8 months ago by • 0
2
votes
3
replies
297
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 8 months ago by 43k • written 8 months ago by ▴ 40
0
votes
2
replies
195
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 8 months ago by ▴ 30 • written 8 months ago by ▴ 120
0
votes
3
replies
566
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind normalization
updated 8 months ago by ★ 4.0k • written 5.1 years ago by • 0
1
vote
4
replies
912
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 8 months ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
1
reply
273
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 8 months ago by 13k • written 2.1 years ago by • 0
0
votes
10
replies
453
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 8 months ago by 33k • written 8 months ago by ▴ 10
1
vote
8
replies
482
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
9 months ago • updated 8 months ago Hesh • 0
1
vote
1
reply
467
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 9 months ago by ★ 4.0k
7
votes
8
replies
732
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
5
replies
262
views
DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2 normalization
updated 9 months ago by 33k • written 9 months ago by • 0
2
votes
7
replies
431
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 9 months ago by ▴ 750 • written 9 months ago by • 0
1
vote
5
replies
215
views
DESeq2 library composition adjustment in size factors
deseq2 normalization
updated 9 months ago by 33k • written 9 months ago by • 0
1
vote
5
replies
200
views
technical replicates and normalization/log transformation
deseq2 normalization
updated 10 months ago by 33k • written 10 months ago by ▴ 40
0
votes
2
replies
174
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 10 months ago by 3.2k • written 10 months ago by • 0
1
vote
2
replies
149
views
tcga and geo train and validation sets
deseq2 normalization
updated 10 months ago by 33k • written 10 months ago by • 0
0
votes
2
replies
184
views
How to normalise data in ballgown?
r normalization edger
updated 10 months ago by 57k • written 10 months ago by • 0
2
votes
4
replies
297
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 11 months ago by 33k • written 11 months ago by • 0
6
votes
13
replies
780
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 11 months ago by 43k • written 11 months ago by ▴ 50
2
votes
3
replies
229
views
Differential gene expression using Ballgown
r normalization
11 months ago lakshmi9c • 0
1
vote
2
replies
153
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 11 months ago by 33k • written 11 months ago by • 0
2
votes
8
replies
416
views
Differential gene expression using R
deseq2 edger normalization limma
updated 11 months ago by 43k • written 11 months ago by • 0
2
votes
4
replies
1.2k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 11 months ago by 3.2k • written 11 months ago by ▴ 40
2
votes
2
replies
177
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 11 months ago by 57k • written 11 months ago by • 0
0
votes
1
reply
130
views
Input of tscR
microarray normalization tscR time-course
updated 12 months ago by 3.2k • written 12 months ago by • 0
0
votes
0
replies
155
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
12 months ago abf ▴ 30
0
votes
2
replies
189
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
2
votes
6
replies
361
views
Question: Method to get normalize allele specific read counts
edger normalization
updated 13 months ago by ★ 27k • written 13 months ago by • 0
0
votes
0
replies
101
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN normalization
13 months ago tofukaj • 0
7
votes
10
replies
342
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 13 months ago by 43k • written 13 months ago by • 0
50 results • Page 1 of 1
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Comment: Best practice for quantifying sncRNA by Abhishek • 0
I wonder what would be a good metric to assess the quantification quality
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for sharing your thoughts. I used Salmon and indexed using hg38 gencodes transcriptome. After the tximport step, I ended up gett…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx so much for the diagnosis and advice. Indeed, in my data, some genes have all 0 for all sampes of a contrast for both "Mut" and "WT" gr…
Comment: Best practice for quantifying sncRNA by Steve Lianoglou 13k
> It's my opinion that miRNA is a mirage intended to make MDs salivate and biostatisticians wail in misery, but what do I know? I'll tell …
Comment: Idea: Using DESeq2 to test a change in ratio of two genes by Michael Love 33k
Yes, it's true that we take the reference gene(s) as a noise free measurement of the reference variation with this approach, and control ag…
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Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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