Showing : spikein • reset
6
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2
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2.4k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 19 months ago by ★ 4.4k • written 19 months ago by ▴ 10
6
votes
12
replies
4.4k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 11 months ago by • 0 • written 3.6 years ago by • 0
3
votes
4
replies
2.1k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
21 months ago • updated 20 months ago spg • 0
1
vote
2
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715
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DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
18 months ago Weisheng • 0
1
vote
9
replies
3.5k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 22 months ago by ▴ 670 • written 3.9 years ago by ▴ 10
0
votes
2
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1.3k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.2 years ago • updated 3.1 years ago maria.soler • 0
0
votes
0
replies
211
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
5 months ago Virangika • 0
0
votes
1
reply
327
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
0
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0
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826
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
3.1 years ago mb1996 • 0
0
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0
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1.0k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.0 years ago Drew • 0
0
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2
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251
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 4 weeks ago by • 0
0
votes
2
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2.0k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 4 months ago by • 0 • written 20 months ago by ▴ 10
12 results • Page 1 of 1
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Comment: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
What does `sampleid` represent? If you use duplicateCorrelation(), then the blocking factor should be subject, it isn't clear from your que…
Answer: Question on performing ANOVA-like analysis using limma by Gordon Smyth 51k
In time course experiments such as this, it is essential to account for baseline variability between subjects, so the second analysis given…
Comment: AffylmGUI does not start wit R 4.4.1 by Gordon Smyth 51k
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Answer: rtracklayer accessing UCSC data table not working by James W. MacDonald 67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome by James W. MacDonald 67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
Votes
Comment: AffylmGUI does not start wit R 4.4.1
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
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