Showing: differential expression • reset
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates written 22 hours ago by Nik dAK • 10
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is our edgeR code doing what we think it does?
edger differential expression rna-seq written 16 days ago by acs1990 • 10 • updated 16 days ago by Yunshun Chen • 460
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Minimum number of cells required for the MAST
differential expression scrnaseq mast written 16 days ago by Andrew_McDavid • 190
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 15 months ago by emi.sch • 10 • updated 10 weeks ago by yusuf.zhc • 0
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Majority upregulated genes in edgeR
edger differential expression genes fold change written 12 weeks ago by ilovesuperheroes1993 • 0 • updated 12 weeks ago by Aaron Lun • 24k
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression design batch correction written 3 months ago by wunderl • 20 • updated 3 months ago by Michael Love ♦ 25k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction written 3 months ago by wunderl • 20 • updated 3 months ago by Michael Love ♦ 25k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
normalization edger differential expression rna-seq fitted values written 3 months ago by David Rengel • 70 • updated 3 months ago by Gordon Smyth ♦ 38k
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How does limma calculate the log2fc?
limma differential expression time-course analysis written 4 months ago by mcfarn1 • 0 • updated 4 months ago by Gordon Smyth ♦ 38k
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How to normalize RNA-seq when 50% genes are DE? (TMM)
rnaseq normalization limma differential expression tmm written 5 months ago by natalia_lt • 0 • updated 5 months ago by James W. MacDonald ♦ 51k
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
differential expression scran single-cell mnn_correct written 6 months ago by baldissera152 • 0
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Limma - Using removeBatchEffect before differential expression analysis
limma differential expression batch effect written 6 months ago by jmoon1194 • 0 • updated 6 months ago by James W. MacDonald ♦ 51k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
differential expression rna-seq peer hidden confounders written 7 months ago by rodrigo.duarte88 • 20 • updated 7 months ago by Martin Morgan ♦♦ 23k
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How to handle replicates and treatment conditions in TissueEnrich package
differential expression rna-seq tissueenrich tissue-specific expression written 8 months ago by andrew.oler • 0 • updated 8 months ago by Ashish Jain • 0
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva differential expression gene set enrichment plage written 8 months ago by krassowski.michal • 0
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Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 12 months ago by Darklings • 0 • updated 12 months ago by Gordon Smyth ♦ 38k
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ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 differential expression rna-seq single cell zinb-wave written 13 months ago by rory.kirchner • 60 • updated 13 months ago by Michael Love ♦ 25k
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Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 14 months ago by Leon • 0 • updated 14 months ago by davide risso • 830
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venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 14 months ago by A • 40 • updated 14 months ago by James W. MacDonald ♦ 51k
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DE analysis when large portion of transcriptome is changed
edger ebseq differential expression rna-seq written 14 months ago by marhabaie • 0 • updated 14 months ago by Aaron Lun • 24k
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Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 15 months ago by Mbosio85 • 0 • updated 15 months ago by Michael Love ♦ 25k
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 differential expression tximport rsem sequence length normalization written 15 months ago by al-ash • 20 • updated 15 months ago by Michael Love ♦ 25k
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pair wise ballgown
differential expression ballgown written 15 months ago by zoe.ward • 0
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 15 months ago by manuelmendoza • 0
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differential expression analysis with big dataset and >500 surrogate variables
sva deseq2 differential expression lrt written 16 months ago by aec • 40
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