Showing: differential expression • reset
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Detecting the power in differential expression
limma edger deseq2 differential expression power written 1 day ago by Beginner • 0 • updated 1 day ago by James W. MacDonald ♦ 51k
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression written 3 days ago by A • 0
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GDCprepare error in TCGAbiolinks
differential expression tcgabiolinks gdcprepare written 27 days ago by fawazfebin • 30
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dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and manual
limma differential expression repeated measures variancepartition dream written 5 weeks ago by hermidalc • 0 • updated 5 weeks ago by Gordon Smyth ♦ 39k
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Multiple samples per individual and unbalanced number of samples per individual: DE between groups still an ordinary two-group comparison?
limma edger deseq2 differential expression repeated measures written 5 weeks ago by hermidalc • 0
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
rnaseq limma R differential expression tpm written 6 weeks ago by atakanekiz • 30 • updated 6 weeks ago by Steve Lianoglou ♦ 12k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates written 8 weeks ago by Nik dAK • 10 • updated 7 weeks ago by Michael Love ♦ 26k
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is our edgeR code doing what we think it does?
edger differential expression rna-seq written 10 weeks ago by acs1990 • 10 • updated 10 weeks ago by Yunshun Chen • 530
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Minimum number of cells required for the MAST
differential expression scrnaseq mast written 10 weeks ago by Andrew_McDavid • 190
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 17 months ago by emi.sch • 20 • updated 4 months ago by yusuf.zhc • 0
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Majority upregulated genes in edgeR
edger differential expression genes fold change written 4 months ago by ilovesuperheroes1993 • 0 • updated 4 months ago by Aaron Lun • 25k
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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 5 months ago by wunderl • 20 • updated 5 months ago by Michael Love ♦ 26k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction written 5 months ago by wunderl • 20 • updated 5 months ago by Michael Love ♦ 26k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
normalization edger differential expression rna-seq fitted values written 5 months ago by David Rengel • 70 • updated 5 months ago by Gordon Smyth ♦ 39k
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How does limma calculate the log2fc?
limma differential expression time-course analysis written 5 months ago by mcfarn1 • 0 • updated 5 months ago by Gordon Smyth ♦ 39k
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How to normalize RNA-seq when 50% genes are DE? (TMM)
rnaseq normalization limma differential expression tmm written 7 months ago by natalia_lt • 0 • updated 7 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 8 months ago by baldissera152 • 0
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Limma - Using removeBatchEffect before differential expression analysis
limma differential expression batch effect written 8 months ago by jmoon1194 • 0 • updated 8 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 9 months ago by rodrigo.duarte88 • 20 • updated 9 months ago by Martin Morgan ♦♦ 24k
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How to handle replicates and treatment conditions in TissueEnrich package
differential expression rna-seq tissueenrich tissue-specific expression written 10 months ago by andrew.oler • 0 • updated 10 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 10 months ago by krassowski.michal • 0
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Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 14 months ago by mico • 0 • updated 14 months ago by Gordon Smyth ♦ 39k
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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 15 months ago by rory.kirchner • 60 • updated 15 months ago by Michael Love ♦ 26k
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Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 16 months ago by Leon • 0 • updated 16 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 16 months ago by A • 40 • updated 16 months ago by James W. MacDonald ♦ 51k
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