Showing : normalization • reset
1
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12
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189
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Data normalization
DESeq2 Normalization
8 days ago • updated 6 days ago nolwenn • 0
0
votes
1
reply
61
views
DESEQ2 normalization for time series data
DESeq2 Normalization Medianofratios
updated 26 days ago by 32k • written 26 days ago by • 0
3
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3
replies
134
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4 weeks ago • updated 29 days ago Federico Alessandro • 0
0
votes
3
replies
160
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by 32k • written 6 weeks ago by • 0
0
votes
1
reply
75
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 6 weeks ago by 2.7k • written 6 weeks ago by • 0
2
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2
replies
97
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 8 weeks ago by ▴ 570 • written 8 weeks ago by • 0
0
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0
replies
81
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
11 weeks ago wrzl • 0
1
vote
3
replies
128
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Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 3 months ago by 32k • written 3 months ago by • 0
0
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1
reply
92
views
error using cqn package
Normalization cqn
updated 4 months ago by 56k • written 4 months ago by ▴ 30
2
votes
2
replies
128
views
Normalisation in DESeq2
DESeq2 Normalization
4 months ago Bine ▴ 10
1
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2
replies
172
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 4 months ago by 32k • written 4 months ago by • 0
2
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3
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189
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 4 months ago by 42k • written 4 months ago by ▴ 40
0
votes
2
replies
120
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 4 months ago by ▴ 30 • written 4 months ago by ▴ 120
0
votes
3
replies
494
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind normalization
updated 5 months ago by ★ 3.8k • written 4.8 years ago by • 0
1
vote
4
replies
824
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5 months ago by ★ 3.8k • written 3.2 years ago by • 0
0
votes
1
reply
209
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 5 months ago by 13k • written 22 months ago by • 0
0
votes
10
replies
260
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Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 5 months ago by 32k • written 5 months ago by ▴ 10
1
vote
8
replies
336
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
5 months ago Hesh • 0
1
vote
1
reply
300
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5 months ago by ★ 3.8k
7
votes
8
replies
384
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 5 months ago by 42k • written 5 months ago by • 0
1
vote
5
replies
184
views
DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2 normalization
updated 5 months ago by 32k • written 5 months ago by • 0
2
votes
7
replies
294
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 6 months ago by ▴ 720 • written 6 months ago by • 0
1
vote
5
replies
144
views
DESeq2 library composition adjustment in size factors
deseq2 normalization
updated 6 months ago by 32k • written 6 months ago by • 0
1
vote
5
replies
122
views
technical replicates and normalization/log transformation
deseq2 normalization
updated 6 months ago by 32k • written 6 months ago by ▴ 40
0
votes
2
replies
121
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 7 months ago by 2.7k • written 7 months ago by • 0
1
vote
2
replies
99
views
tcga and geo train and validation sets
deseq2 normalization
updated 7 months ago by 32k • written 7 months ago by • 0
0
votes
2
replies
117
views
How to normalise data in ballgown?
r normalization edger
updated 7 months ago by 56k • written 7 months ago by • 0
2
votes
4
replies
146
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 7 months ago by 32k • written 7 months ago by • 0
6
votes
13
replies
476
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 7 months ago by 42k • written 7 months ago by ▴ 50
2
votes
3
replies
144
views
Differential gene expression using Ballgown
r normalization
7 months ago lakshmi9c • 0
1
vote
2
replies
100
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 8 months ago by 32k • written 8 months ago by • 0
2
votes
8
replies
293
views
Differential gene expression using R
deseq2 edger normalization limma
updated 8 months ago by 42k • written 8 months ago by • 0
2
votes
4
replies
705
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 8 months ago by 2.7k • written 8 months ago by ▴ 30
2
votes
2
replies
104
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 8 months ago by 56k • written 8 months ago by • 0
0
votes
1
reply
84
views
Input of tscR
microarray normalization tscR time-course
updated 8 months ago by 2.7k • written 8 months ago by • 0
0
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0
replies
107
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
8 months ago abf ▴ 30
0
votes
2
replies
111
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 8 months ago by ★ 3.8k • written 8 months ago by • 0
2
votes
6
replies
255
views
Question: Method to get normalize allele specific read counts
edger normalization
updated 9 months ago by ★ 26k • written 9 months ago by • 0
0
votes
0
replies
58
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN normalization
9 months ago tofukaj • 0
7
votes
10
replies
197
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 10 months ago by 42k • written 10 months ago by • 0
2
votes
1
reply
150
views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
updated 10 months ago by 32k • written 10 months ago by • 0
4
votes
10
replies
187
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 11 months ago by 2.7k • written 11 months ago by ▴ 10
0
votes
1
reply
132
views
DESeq2 and Heatmap for multiple conditions
deseq2 normalization
updated 11 months ago by 32k • written 11 months ago by ▴ 20
2
votes
7
replies
222
views
ControlGenes/ housekeeping genes Deseq2
normalization deseq2 sizefactors
updated 11 months ago by 32k • written 11 months ago by ▴ 20
4
votes
3
replies
987
views
How to plot the batch corrected values in DESeq2
deseq2 normalization
updated 11 months ago by 32k • written 2.3 years ago by • 0
1
vote
4
replies
632
views
pheatmap for DEGs
normalization pheatmap
updated 11 months ago by 2.7k • written 11 months ago by ▴ 20
0
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2
replies
170
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2 edgeR repenrich2 normalization
11 months ago mkmwong • 0
0
votes
3
replies
70
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2 normalization
updated 12 months ago by 32k • written 12 months ago by • 0
0
votes
2
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79
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2 normalization
updated 12 months ago by • 0 • written 12 months ago by • 0
0
votes
3
replies
87
views
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
normalization
updated 12 months ago by 42k • written 12 months ago by • 0
1,643 results • Page 1 of 33
Recent ...
Replies
Answer: DepMap copy number by Laurent Gatto 1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp by James W. MacDonald 56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq by Naomi Altman ★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile by Mike Smith ★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db by Xulei Huo • 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
Awards • All
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