Showing : Normalization • reset
0
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5
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141
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Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 1 day ago by 33k • written 20 days ago by • 0
1
vote
1
reply
82
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 15 days ago by ▴ 870 • written 22 days ago by ▴ 10
2
votes
2
replies
96
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
5 weeks ago • updated 4 weeks ago geoffrey ▴ 10
0
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4
replies
159
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
7 weeks ago • updated 6 weeks ago Yuqia • 0
0
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0
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75
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Cross-cultivar RNA-seq analysis
RNA Normalization
7 weeks ago nancy • 0
1
vote
12
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310
views
Data normalization
DESeq2 Normalization
10 weeks ago • updated 9 weeks ago nolwenn • 0
0
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1
reply
100
views
DESEQ2 normalization for time series data
DESeq2 Normalization Medianofratios
updated 12 weeks ago by 33k • written 12 weeks ago by • 0
3
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3
replies
201
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
3 months ago Federico Alessandro • 0
0
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3
replies
224
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 3 months ago by 33k • written 3 months ago by • 0
0
votes
1
reply
112
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 3 months ago by 3.1k • written 3 months ago by • 0
2
votes
2
replies
154
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4 months ago by ▴ 640 • written 4 months ago by • 0
0
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0
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115
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
4 months ago wrzl • 0
1
vote
3
replies
175
views
Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 5 months ago by 33k • written 5 months ago by • 0
0
votes
1
reply
125
views
error using cqn package
Normalization cqn
updated 6 months ago by 57k • written 6 months ago by ▴ 30
2
votes
2
replies
162
views
Normalisation in DESeq2
DESeq2 Normalization
6 months ago Bine ▴ 10
1
vote
2
replies
209
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 6 months ago by 33k • written 6 months ago by • 0
2
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3
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259
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 6 months ago by 43k • written 7 months ago by ▴ 40
0
votes
2
replies
168
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 7 months ago by ▴ 30 • written 7 months ago by ▴ 120
0
votes
3
replies
539
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind normalization
updated 7 months ago by ★ 3.9k • written 5.0 years ago by • 0
1
vote
4
replies
872
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 7 months ago by ★ 3.9k • written 3.4 years ago by • 0
0
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1
reply
246
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 7 months ago by 13k • written 2.0 years ago by • 0
0
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10
replies
397
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 7 months ago by 33k • written 7 months ago by ▴ 10
1
vote
8
replies
420
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
7 months ago Hesh • 0
1
vote
1
reply
401
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 7 months ago by ★ 3.9k
7
votes
8
replies
602
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
5
replies
238
views
DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2 normalization
updated 8 months ago by 33k • written 8 months ago by • 0
2
votes
7
replies
390
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 8 months ago by ▴ 750 • written 8 months ago by • 0
1
vote
5
replies
181
views
DESeq2 library composition adjustment in size factors
deseq2 normalization
updated 8 months ago by 33k • written 8 months ago by • 0
1
vote
5
replies
168
views
technical replicates and normalization/log transformation
deseq2 normalization
updated 9 months ago by 33k • written 9 months ago by ▴ 40
0
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2
replies
157
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 3.1k • written 9 months ago by • 0
1
vote
2
replies
120
views
tcga and geo train and validation sets
deseq2 normalization
updated 9 months ago by 33k • written 9 months ago by • 0
0
votes
2
replies
159
views
How to normalise data in ballgown?
r normalization edger
updated 9 months ago by 57k • written 9 months ago by • 0
2
votes
4
replies
236
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 9 months ago by 33k • written 9 months ago by • 0
6
votes
13
replies
667
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 9 months ago by 43k • written 9 months ago by ▴ 50
2
votes
3
replies
197
views
Differential gene expression using Ballgown
r normalization
9 months ago lakshmi9c • 0
1
vote
2
replies
133
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 10 months ago by 33k • written 10 months ago by • 0
2
votes
8
replies
366
views
Differential gene expression using R
deseq2 edger normalization limma
updated 10 months ago by 43k • written 10 months ago by • 0
2
votes
4
replies
1.0k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 10 months ago by 3.1k • written 10 months ago by ▴ 40
2
votes
2
replies
139
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 10 months ago by 57k • written 10 months ago by • 0
0
votes
1
reply
111
views
Input of tscR
microarray normalization tscR time-course
updated 10 months ago by 3.1k • written 10 months ago by • 0
0
votes
0
replies
138
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
10 months ago abf ▴ 30
0
votes
2
replies
158
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 10 months ago by ★ 3.9k • written 11 months ago by • 0
2
votes
6
replies
321
views
Question: Method to get normalize allele specific read counts
edger normalization
updated 11 months ago by ★ 26k • written 11 months ago by • 0
0
votes
0
replies
85
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN normalization
11 months ago tofukaj • 0
7
votes
10
replies
285
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 12 months ago by 43k • written 12 months ago by • 0
2
votes
1
reply
179
views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
updated 12 months ago by 33k • written 12 months ago by • 0
4
votes
10
replies
297
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 13 months ago by 3.1k • written 13 months ago by ▴ 10
0
votes
1
reply
218
views
DESeq2 and Heatmap for multiple conditions
deseq2 normalization
updated 13 months ago by 33k • written 13 months ago by ▴ 20
2
votes
7
replies
345
views
ControlGenes/ housekeeping genes Deseq2
normalization deseq2 sizefactors
updated 13 months ago by 33k • written 13 months ago by ▴ 20
4
votes
3
replies
1.1k
views
How to plot the batch corrected values in DESeq2
deseq2 normalization
updated 13 months ago by 33k • written 2.4 years ago by • 0
50 results • Page 1 of 1
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Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Comment: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
They are actually rounded to zero in the `dds` which requires integer values.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
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