Showing : Contrasts • reset
2
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8
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272
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
9 weeks ago • updated 8 weeks ago Jane • 0
3
votes
8
replies
331
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 19 months ago by 57k • written 19 months ago by • 0
0
votes
1
reply
296
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 19 months ago by 33k • written 19 months ago by • 0
0
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0
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143
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
19 months ago ingerslev • 0
0
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1
reply
264
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 20 months ago by 33k • written 20 months ago by • 0
2
votes
3
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330
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 20 months ago by 33k • written 20 months ago by ▴ 140
0
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4
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258
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
1
reply
229
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 2.2 years ago by 33k • written 2.2 years ago by • 0
3
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5
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481
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 30
2
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6
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356
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
10 results • Page 1 of 1
Recent ...
Replies
Answer: Using both spike in and TMM normalizations in ChIP-seq samples by Gordon Smyth 43k
It is impossible to use both spike-in or TMM normalization. You must do one or the other. They replace each other, they cannot be combined.…
Comment: Best practice for quantifying sncRNA by ATpoint ▴ 700
If the sequences are 20-something bp long then it appears logical to me to throw away any reads that are longer than that after adapter tri…
Comment: P value and Adj. P value showing N/A by ATpoint ▴ 700
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na As Mike says, you can be…
Comment: Using both spike in and TMM normalizations in ChIP-seq samples by ATpoint ▴ 700
I just gave my two cents on spike-ins and normalization diagnostic over at biostars (see link below) which you may want to have a look at. …
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
You may well get lots of protein coding genes, depending on what's in the transcripts file. Do note that most miRNA transcripts are complem…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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