Showing : SpikeIn • reset
4
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1.7k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 6 months ago by • 0 • written 3.2 years ago by • 0
3
votes
4
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1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago • updated 15 months ago spg • 0
1
vote
2
replies
577
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DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
13 months ago Weisheng • 0
1
vote
9
replies
3.0k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 17 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
0
votes
0
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76
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
8 days ago Virangika • 0
0
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0
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695
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
0
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0
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896
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.5 years ago Drew • 0
0
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1
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1.3k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 15 months ago by 41k • written 15 months ago by ▴ 10
0
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2
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1.1k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.7 years ago maria.soler • 0
10 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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