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tximport
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edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
15 days ago
Marianna
▴ 20
0
votes
2
replies
182
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 23 days ago by
Michael Love
41k • written 23 days ago by
SG
• 0
6
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8
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1.5k
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Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 6 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
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Answer: Log-cpm values from limma
by
Gordon Smyth
50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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