Showing : Normalization • reset
0
votes
2
replies
1.1k
views
How to normalise data in ballgown?
r normalization edger
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
3
votes
4
replies
4.4k
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
6
votes
13
replies
7.9k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 3.4 years ago by 53k • written 5.3 years ago by ▴ 60
2
votes
3
replies
1.4k
views
Differential gene expression using Ballgown
r normalization
5.3 years ago lakshmi9c • 0
1
vote
2
replies
767
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
8
replies
2.8k
views
Differential gene expression using R
deseq2 edger normalization limma
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
2
votes
4
replies
12k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 60
2
votes
2
replies
1.9k
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
0
votes
1
reply
886
views
Input of tscR
microarray normalization tscR time-course
updated 5.3 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
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0
replies
850
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.4 years ago abf ▴ 30
0
votes
2
replies
1.7k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 5.4 years ago by ★ 5.2k • written 5.4 years ago by • 0
2
votes
6
replies
1.7k
views
Question: Method to get normalize allele specific read counts
edger normalization
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
0
votes
0
replies
766
views
According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBN normalization
5.4 years ago tofukaj • 0
7
votes
10
replies
3.0k
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 20
2
votes
1
reply
1.8k
views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
4
votes
10
replies
4.3k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
DESeq2 and Heatmap for multiple conditions
deseq2 normalization
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
4
votes
7
replies
4.8k
views
ControlGenes/ housekeeping genes Deseq2
normalization deseq2 sizefactors
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
4
votes
5
replies
3.7k
views
How to plot the batch corrected values in DESeq2
deseq2 normalization
updated 4.3 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
replies
13k
views
pheatmap for DEGs
normalization pheatmap
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 20
0
votes
2
replies
1.3k
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2 edgeR repenrich2 normalization
5.6 years ago mkmwong • 0
0
votes
3
replies
705
views
Unbalanced design and large difference in number of input reads for DESeq2
deseq2 normalization
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
2
replies
1.6k
views
Error in DESeqDataSet: variables and colnames don't match when they do
deseq2 normalization
updated 5.6 years ago by • 0 • written 5.6 years ago by • 0
0
votes
3
replies
2.1k
views
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
normalization
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
votes
1
reply
1.4k
views
Removing low sequences before analysis
deseq2 normalization
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
1
reply
720
views
Length scaled TPM and orthologous genes, from Tximport package
normalization
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
votes
8
replies
6.4k
views
Combining 2 datasets from 2 different RNAseq experiments
deseq2 normalization probe
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
4
replies
1.9k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ★ 2.0k
0
votes
3
replies
764
views
DEseq2 design tutorial with multiple experimental factors
deseq2 annotation normalization
5.7 years ago christophe.vanhaver • 0
2
votes
1
reply
1.8k
views
Using DESeq2 for normalization of dataset with no replicates
normalization deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
0
replies
515
views
DESeq2 analysis with scaled continues variables
normalization
5.7 years ago adR ▴ 40
1
vote
3
replies
1.2k
views
DE analysis outlier removal
deseq2 outlier normalization removal
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
2
replies
1.1k
views
Data not getting normalised after DESeq2
deseq2 normalization
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
1
vote
1
reply
934
views
a package with randomization/permutation tests for genomic analyses
normalization
5.8 years ago Bogdan ▴ 670
1
vote
5
replies
658
views
Microarray expression analysis
normalization
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
4
replies
819
views
Microarray expression analysis
normalization
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
2
replies
1.3k
views
Normalization and dispersion estimates in timeseries data with highly variable read numbers
EdgeR dispersion normalization
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
1
vote
1
reply
2.5k
views
How to annotate the Affymetrix data HTA-2.0 with oligo
annotation affy normalization
updated 5.8 years ago by ★ 4.1k • written 5.8 years ago by • 0
2
votes
2
replies
1.7k
views
Microarray expression analysis
microarray normalization CEL.gz
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
13
replies
2.1k
views
DESeq2 normalization resulting in very different Total read counts for samples
deseq2 normalization
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
3
replies
1.6k
views
TMM normalisation on metatranscriptome data: for visualisation/fold-change only
normalization edgeR metatranscriptome
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
0
votes
2
replies
2.3k
views
How should I normalize my RNAseq data from Polysome profiling
deseq2 bioconductor RNAseq normalization Polysome_profiling
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
6
votes
5
replies
4.1k
views
VST for scRNA-seq
deseq2 rnaseq normalization
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 50
0
votes
4
replies
1.2k
views
Normalizing for both gene size and library composition
RNA-seq normalization deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
3
votes
2
replies
3.7k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 10
1
vote
2
replies
592
views
DESeq2 input data.
DESeq2 Normalization Input data
5.9 years ago Fischer-philipp ▴ 30
0
votes
0
replies
1.0k
views
cqn vignette error
cqn normalization edger
6.0 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
1.0k
views
Normalized counts access in DESeq2 R: with and without batch
deseq2 edger normalization
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
0
votes
3
replies
1.2k
views
DESeq2 standalone TE usage
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.9k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 6.0 years ago by • 0 • written 6.9 years ago by ★ 4.1k
1,761 results • Page 4 of 36
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
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Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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