Showing : normalization • reset
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Where can we find the sample data i.e. "test.expressiondata.txt" used in the TissueEnrich? It is showing error with my data "Error in read.table....l…
normalization tissue-specific genes TissueEnrich Package
updated 6.8 years ago by 4.3k • written 6.8 years ago by • 0
0
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2
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1.6k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 10
2
votes
8
replies
2.3k
views
Cydar normalizeBatch specifying batches
Cydar normalization normalizeBatch
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 10
1
vote
1
reply
1.5k
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
3
votes
5
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1.2k
views
Differential Expression Analysis for Single Population RNASeq in Deseq2
deseq2 normalization
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
replies
1.9k
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC probe normalization GEOdata cancer
6.9 years ago s.goncalvesclaro ▴ 10
0
votes
7
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1.2k
views
Unexpected p-values by DESeq2
deseq2 normalization
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
1
reply
2.1k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 10
6
votes
7
replies
1.9k
views
Appropriate experimental design for differential expresion
edgeR normalization cancer
updated 6.9 years ago by ★ 1.4k • written 6.9 years ago by ▴ 20
3
votes
5
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18k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 2.3 years ago by • 0 • written 7.2 years ago by • 0
0
votes
1
reply
762
views
Applying external size factors to a dds did not yield expected results
DESeq2 normalization size factors
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 10
2
votes
2
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1.6k
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 6.9 years ago by ★ 29k • written 6.9 years ago by • 0
0
votes
1
reply
712
views
an error with NormalizeBeta
normalization
6.9 years ago binli1765 • 0
1
vote
3
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1.8k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 6.9 years ago by ★ 6.5k • written 6.9 years ago by • 0
1
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1
reply
1.1k
views
Valid to normalise MethylumiSet using minfi?
normalization minfi methylumi
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
2
votes
6
replies
2.7k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
0
votes
2
replies
1.1k
views
genomicFeature---paired end read::reads from the same pair were found not adjacent to each
normalization
updated 7.0 years ago by 25k • written 7.0 years ago by • 0
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0
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853
views
ChAMP champ.norm BMIQ produces differing results
microarray normalization
7.0 years ago Gurkenkönig ▴ 10
4
votes
6
replies
4.8k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 70
0
votes
2
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2.5k
views
Heatmap of RPKM analysis
normalization
updated 7.0 years ago by ★ 4.0k • written 7.0 years ago by • 0
0
votes
1
reply
974
views
Normalization large data set
normalization gcRMA
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
8
votes
4
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3.6k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin edgeR deseq2 normalization rnaseq
updated 7.0 years ago by ★ 7.9k • written 7.0 years ago by ▴ 90
2
votes
3
replies
985
views
Recommendations for normalisation post-deseq2
deseq2 normalization posthoc
7.0 years ago marc.osullivan • 0
1
vote
1
reply
1.1k
views
Normalized counts from DESeq2 results in similar but not equal total read count?
deseq2 normalization
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
votes
1
reply
1.3k
views
Highly uneven mapping rates and counts between samples
limma normalization deseq2
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 420
0
votes
4
replies
1.8k
views
varianceStabilizingTransformation for clustering, deconvolution
deseq2 deconvolution normalization limma
updated 7.0 years ago by 43k • written 7.1 years ago by ▴ 30
0
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2
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1.0k
views
Error in Champ for Bioconductor analysis 450K methylation data
normalization
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
0
votes
0
replies
718
views
Error in Champ for Bioconductor and ChAMP.Block() analysis 450K methylation data
normalization microarray
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
5
votes
10
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5.7k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
12
votes
10
replies
10.0k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
7.9 years ago • updated 7.1 years ago rached ▴ 60
0
votes
1
reply
1.1k
views
RUV integration in DESeq2 design
deseq2 normalization
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
3
votes
4
replies
2.8k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 30
2
votes
5
replies
3.2k
views
Deseq normalization with adjusting gene length
deseq2 normalization
7.2 years ago Maryam • 0
0
votes
3
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1.6k
views
Reverse Normalized RNA-seq readcounts/fpkm values to raw readcounts
RNA-seq deseq2 normalization readcount reverse
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
3
votes
5
replies
2.2k
views
Normalization for small non-coding RNA and multi-factor design
edger limma voom normalization limma
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 90
0
votes
3
replies
4.8k
views
Data normalization and transformation using DESeq2
deseq2 normalization rnaseq rlog transformation variancestabilizingtransformation
7.2 years ago chiara.facciotto • 0
0
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1
reply
787
views
Issue with normalization in DESeq2
deseq2 normalization rnaseq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
3
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1.4k
views
TMM normalization of cancer RNA seq
cancer normalization
updated 7.3 years ago by ★ 13k • written 7.3 years ago by • 0
0
votes
3
replies
1.4k
views
normalization of ChIP-seq data
normalization chip-seq
7.3 years ago Bogdan ▴ 670
6
votes
4
replies
6.9k
views
Method to get normalized counts in edgeR without cpm
edger normalization
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 20
0
votes
4
replies
1.6k
views
DESeq2 MA plot normalisation Issue
deseq2 normalization maplot rnaseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
vote
4
replies
778
views
How to monitor the performance of MS-based omics data?
normalization
updated 7.3 years ago by • 0 • written 7.3 years ago by ▴ 10
1
vote
2
replies
1.5k
views
genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
0
votes
1
reply
1.6k
views
Normalization and Quality Control for Multiple scRNAseq Data Sets
normalization rnaseq genetics batch effect dropout
updated 7.3 years ago by ★ 13k • written 7.3 years ago by • 0
0
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2
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3.1k
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ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
7.4 years ago yuabrahamliu • 0
0
votes
2
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1.1k
views
DESeq2 normalization Factor Matrix to correct for uneven targeted sequencing coverage
deseq2 normalization
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
votes
4
replies
5.2k
views
DESeq2- Size factors (median of ratios) assumptions - global adjustment normalization?
deseq2 quantro normalization
7.4 years ago Victor Barrera • 0
0
votes
7
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2.2k
views
DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
1
vote
2
replies
942
views
Normalize the raw data from multiple studies
normalization affy
7.4 years ago mahm ▴ 20
4
votes
13
replies
3.3k
views
Why is batch effect correction an option in SCAN.UPC normalization?
scan.upc upc normalization batch effect correction
updated 7.5 years ago by ▴ 600 • written 7.5 years ago by • 0
1,762 results • Page 6 of 36
Recent ...
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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