Showing : meta-analysis • reset
0
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What does one-sided p-value in DESeq2 mean in biological terms?
one-sided nbinomWaldTest p-value meta-analysis DESeq2
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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11
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3.8k
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Remove NaN from a list or replace NaN with a value.
R meta-analysis
updated 2.7 years ago by • 0 • written 5.4 years ago by ▴ 10
0
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7
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1.5k
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Problem using load_raw() function in crossmeta R package
cross meta-analysis crossmeta
3.2 years ago michael.s • 0
3
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1
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513
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Meta-Analysis: Start with counts?
meta-analysis
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
1
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2
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834
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Meta-analysis of RNAseq data
RNAseq meta-analysis microarray public data sets
updated 5.2 years ago by ▴ 110 • written 5.2 years ago by ▴ 90
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3
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1.8k
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Algorithm for between and within microarray normalisation (for meta-analysis).
microarray meta-analysis gene expression
updated 5.3 years ago by 0 • written 7.8 years ago by ▴ 70
2
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1
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719
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how do meta-analysis with Na p-value of DESeq2 ?
deseq2 meta-analysis metaseq
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
0
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0
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845
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Meta-Analysis chip-seq data
chip-seq meta-analysis
6.9 years ago rezapanahi222 • 0
0
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0
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793
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tools or package for meta-analysis of chip-seq result
chipseq meta-analysis
6.9 years ago rezapanahi222 • 0
2
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4
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1.6k
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R package for Meta-Analysis of CHIP-Seq data
chipseq meta-analysis ubuntu
6.9 years ago rezapanahi222 • 0
6
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4
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2.9k
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Meta-analysis of microarrays (and RNA-seq) data
meta-analysis
updated 7.0 years ago by ▴ 110 • written 7.0 years ago by ▴ 40
3
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6
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1.3k
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Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
microarray rnaseq DEgenes meta-analysis limma
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 830
0
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1
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1.0k
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meta analysis of p value data by metaseq package
rnaseq meta-analysis p values
7.3 years ago hassangiahi • 0
0
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1
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930
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Meta-analysis on rna-seq data without replicates
meta-analysis rnaseq metarnaseq
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 10
2
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5
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2.6k
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Question on how to proceed and analyze 9 microarray datasets of two different platforms to perform meta-analysis
microarray meta-analysis cross-platform normalization statistical inference
updated 7.8 years ago by ▴ 110 • written 8.3 years ago by ▴ 80
3
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6
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2.0k
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Comparison of DE lists from different datasets of same microarray platform
microarray DE-comparison meta-analysis scatter-plot limma
8.1 years ago Konstantinos Yeles ▴ 80
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0
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1.7k
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MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
MetaDE meta-analysis
8.2 years ago alexvpickering ▴ 110
4
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4
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1.3k
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Comparing DE probes from same-platform microarrays
limma microarray meta-analysis
updated 8.3 years ago by 50k • written 8.3 years ago by ▴ 10
4
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1
reply
2.3k
views
Meta-analysis of gene expression data by 'MetaDE'
r meta-analysis MetaDE
updated 8.4 years ago by ▴ 150 • written 8.7 years ago by ▴ 260
2
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4
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2.8k
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Meta-Analysis after running limma on a normalized dataset
meta-analysis limma toptable
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
20 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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