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design formula
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8
votes
3
replies
4.7k
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Understanding interaction term in DESeq2
deseq2
design formula
log fold change
3.8 years ago
jason.taotaotan
▴ 40
0
votes
2
replies
633
views
DESeq2 design formula
deseq2
design formula
updated 4.3 years ago by
swbarnes2
★ 1.3k • written 4.3 years ago by
tracecakes
• 0
1
vote
2
replies
842
views
Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2
rnaseq
repeated measures
time series
design formula
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
Dorien
▴ 10
0
votes
2
replies
975
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
ac_bioinformatics
• 0
0
votes
2
replies
774
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
corinne_hutfilz
• 0
5 results • Page
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Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results
by
ATpoint
★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Ask yourself the question how a gene that is exactly the same everywhere adds anything to any analysis. Heatmaps usually take DEGs to infer…
Votes
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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WouterDeCoster
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Michael Love
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