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SpikeIn
•
reset
1
vote
2
replies
550
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
12 months ago
Weisheng
• 0
4
votes
2
replies
1.6k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
kalavattam
▴ 10
0
votes
1
reply
1.2k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 14 months ago by
Michael Love
41k • written 14 months ago by
kalavattam
▴ 10
3
votes
4
replies
1.5k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
15 months ago • updated 14 months ago
spg
• 0
0
votes
0
replies
870
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
2.5 years ago
Drew
• 0
0
votes
0
replies
677
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
2.6 years ago
mb1996
• 0
0
votes
2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
2.7 years ago • updated 2.6 years ago
maria.soler
• 0
4
votes
12
replies
3.6k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 6 months ago by
Miguel
• 0 • written 3.1 years ago by
robert.chen
• 0
1
vote
9
replies
2.9k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 16 months ago by
Bogdan
▴ 670 • written 3.4 years ago by
Hesh
▴ 10
9 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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