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Correct way to analyze the data/look at significant variations
deseq2 written 2 hours ago by skamboj • 0
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25
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log2foldchange vs density plot from likelihood and posterior
deseq2 written 5 hours ago by n.naharfancy • 0 • updated 3 hours ago by Michael Love ♦ 24k
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DESeq2 "Not full rank" Error
deseq2 written 9 hours ago by DakJackson • 0 • updated 3 hours ago by Michael Love ♦ 24k
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3
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133
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DESeq2 logfoldchange and interaction in model
deseq2 R rna-seq logfoldchange written 6 weeks ago by pierre.marin • 0
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32
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RNASeq biplot variables and samples
rnaseq deseq2 written 1 day ago by ecg1g15 • 0 • updated 20 hours ago by Michael Love ♦ 24k
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RNA-seq time course analysis with only one experimental condition
cancer deseq2 rna-seq time-series written 1 day ago by mah19 • 0
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81
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Comparing two different sequencing method by DEseq2
deseq2 written 3 days ago by n.naharfancy • 0 • updated 2 days ago by swbarnes2 • 220
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63
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DESeq2: name and contrast arguments return partially different results under specific circumstances -- bug?
deseq2 written 4 days ago by Vincent de Bakker • 0 • updated 4 days ago by Michael Love ♦ 24k
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1
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DESeq2 formula to include batch AND patient, and condition ?
deseq2 written 5 days ago by sxv • 0 • updated 4 days ago by Michael Love ♦ 24k
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1
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40
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File type for DEseq using ATACseq data
deseq2 written 4 days ago by mw848 • 0 • updated 4 days ago by Michael Love ♦ 24k
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2
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85
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DESeq2 error on analyzing microbiome data
sequencing microbiome deseq2 written 7 days ago by zhigang.li • 0
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46
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Retrieving Normalized Groups from Results()
deseq2 written 7 days ago by dennism9251 • 0 • updated 6 days ago by Michael Love ♦ 24k
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Should I subsample an over-clustered sample for DESeq2?
deseq2 written 6 days ago by russell.stewart.j • 0 • updated 6 days ago by Michael Love ♦ 24k
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176
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Difference of difference, paired design
limma edger deseq2 written 10 days ago by Bloodgas • 0 • updated 7 days ago by swbarnes2 • 220
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Creating the correct design
deseq2 written 9 days ago by skamboj • 0 • updated 9 days ago by Michael Love ♦ 24k
2
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45
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Using altHypothesis with shrunken LFC values in DESeq2
deseq2 written 9 days ago by zefrieira • 0 • updated 9 days ago by Michael Love ♦ 24k
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1
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76
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Paired samples in cell lines using DESeq2
deseq2 written 9 days ago by Puks • 10 • updated 9 days ago by Michael Love ♦ 24k
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48
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Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
deseq2 design time course basal group written 10 days ago by Rob Buurstede • 0 • updated 9 days ago by Michael Love ♦ 24k
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6 follow
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 13 months ago by emi.sch • 10 • updated 9 days ago by yusuf.zhc • 0
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deseq2 pre filter rna seq
rnaseq deseq2 written 10 days ago by badribio • 0 • updated 9 days ago by zefrieira • 0
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Including sva results in SeqGSEA with data with batch effect
limma deseq sva deseq2 seqgsea written 9 days ago by kentfung • 0
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Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma edger deseq2 written 11 days ago by Ben • 0 • updated 11 days ago by James W. MacDonald ♦ 50k
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41
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Anbiguous instruction on how to set the blind value in DESeq2's vst function
deseq2 written 11 days ago by qlin • 0 • updated 11 days ago by Michael Love ♦ 24k
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Error in summary.DESeqResults(res) : could not find function "summary.DESeqResults"
deseq2 written 13 days ago by lech.kaczmarczyk • 10 • updated 13 days ago by Michael Love ♦ 24k
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1
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More Info on results names
deseq2 written 15 days ago by dennism9251 • 0
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