Showing : gene expression • reset
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DESeq2 # of up-and down-regulated genes are approximately equal
deseq2 gene expression
updated 3.0 years ago by 40k • written 3.0 years ago by • 0
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4
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813
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GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 3.7 years ago by ▴ 320 • written 3.7 years ago by • 0
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686
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
3.8 years ago astridite • 0
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Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
4.0 years ago dezer ▴ 10
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2
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680
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NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.1 years ago by 63k • written 4.1 years ago by • 0
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3
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Differential Expression Analysis in edgeR using Anova
edger anova gene expression Dispersion
updated 4.2 years ago by • 0 • written 4.7 years ago by • 0
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7
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How to read Illumina data used in the MACQ project (GSE5350)
microarray normalization Illumina data MACQ project gene expression
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
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3
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940
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How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
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3
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1.3k
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RPM data analysis with DESeq2
deseq2 RPM gene expression
4.5 years ago ruhollah.mb • 0
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5
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1.5k
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Getting opposite log2 fold change
deseq2 gene expression log2foldchange R
updated 4.6 years ago by 40k • written 4.6 years ago by • 0
1
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Microarray Analysis of Sleep Deprivation Data Experimental Design
limma gene expression r diffeential expression microarray analysis
updated 4.6 years ago by 63k • written 4.6 years ago by • 0
2
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2
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669
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Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 4.7 years ago by 48k • written 4.7 years ago by • 0
2
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3
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747
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How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression enrichment RNA-seq DESeq2
updated 4.7 years ago by 40k • written 4.7 years ago by ▴ 30
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3
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1.7k
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Algorithm for between and within microarray normalisation (for meta-analysis).
microarray meta-analysis gene expression
updated 4.7 years ago by 0 • written 7.2 years ago by ▴ 70
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2
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1.3k
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How can I compare the expression of two genes within the same sample?
gene expression rnaseq deseq2
updated 4.7 years ago by ▴ 30 • written 4.7 years ago by • 0
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557
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problem with DeMAND, gene expression matrix input
DeMAND gene expression
4.9 years ago chipolino • 0
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0
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744
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
5.0 years ago dezer ▴ 10
3
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4
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edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 5.1 years ago by 48k • written 5.1 years ago by • 0
3
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11
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1.9k
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Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.1 years ago by 21k • written 5.1 years ago by ▴ 20
0
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644
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Obtaining gene expression value for a list of genes
gene expression
updated 5.1 years ago by 48k • written 5.1 years ago by ▴ 20
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4
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3.8k
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WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 5.4 years ago by ★ 2.8k • written 5.4 years ago by • 0
0
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2
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838
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Question about Illuminaio
illuminaio illumina human ht-12 v4 gene expression micorarray
updated 5.5 years ago by ★ 6.1k • written 5.5 years ago by • 0
2
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1
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4.3k
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Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 5.6 years ago by 40k • written 5.6 years ago by • 0
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
5.6 years ago jol.espinoz ▴ 40
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907
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Interpreting Affymetrix Human Genome U133 Plus 2.0 samples
gene expression gene expression data cel affy affymatrix
5.7 years ago torgeirous • 0
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Representative gene expression value in one condition with several replicates
rnaseq gene expression edger
updated 5.8 years ago by 48k • written 5.8 years ago by • 0
0
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4
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1.1k
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
5.9 years ago arfranco ▴ 130
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3
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Anova test on gene expression data
Anova gene expression
updated 5.9 years ago by 63k • written 5.9 years ago by • 0
0
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4
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1.0k
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Gene clusters based on gene expression across samples
kmeans gene expression clustering
6.0 years ago • updated 5.9 years ago Jane Merlevede ▴ 90
1
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Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 5.9 years ago by 48k • written 5.9 years ago by • 0
2
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1
reply
862
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gene expression data analysis and batch effect methods
batch effect gene expression
updated 6.3 years ago by ▴ 410 • written 6.3 years ago by • 0
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0
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880
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gene expression data analysis and batch effect methods
batch effect gene expression
6.3 years ago tati6406 • 0
1
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1
reply
5.5k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 6.5 years ago by ★ 2.8k • written 6.5 years ago by ▴ 10
2
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2
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1.2k
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SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
6.7 years ago Brian Smith ▴ 120
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2
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731
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Is there any bioc tool to predict/quantify transcription factor activation using gene expression data?
transcription factor tf activation gene regulatory network gene expression
updated 6.8 years ago by • 0 • written 6.8 years ago by • 0
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0
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933
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Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
6.8 years ago carleshf ▴ 10
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Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
6.9 years ago Jon Bråte ▴ 250
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1.0k
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Help needed to identify common genes among datasets
datasets genes gene expression
updated 8.1 years ago by 13k • written 8.1 years ago by • 0
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2
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2.7k
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barplot with ggplot2 for gene expression
ggplot2 barplot gene expression gene expression
updated 8.1 years ago by 63k • written 8.1 years ago by ▴ 130
39 results • Page 1 of 1
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Answer: shinyMethyl - saving the file by Guillaume Devailly ▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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