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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
just now
glaciya2018
• 0
1
vote
2
replies
45
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
21 hours ago • updated 10 minutes ago
ATpoint
★ 4.0k
0
votes
0
replies
14
views
PCA plot suggestions
DESeq2
PCAtools
4 hours ago
Aaliya
• 0
0
votes
1
reply
67
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 hours ago by
Michael Love
41k • written 14 hours ago by
kcarey
• 0
0
votes
0
replies
14
views
ATACseq merge peaks
DiffBind
15 hours ago • updated 14 hours ago
Shloka
• 0
0
votes
0
replies
13
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Differential splicing from SGSeq analysis
DEXSeq
SGSeq
17 hours ago • updated 16 hours ago
Sara
• 0
2
votes
5
replies
136
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get BM error
ensembldb
updated 16 hours ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
2
votes
3
replies
93
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 18 hours ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
0
votes
0
replies
23
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
19 hours ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
77
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 hours ago by
Michael Love
41k • written 23 hours ago by
andrebolerbarros
▴ 20
0
votes
2
replies
69
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 43 minutes ago
winwater0928
• 0
0
votes
8
replies
176
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
2
replies
96
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 1 hour ago
shuwangxinze1996
• 0
0
votes
5
replies
207
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 17 hours ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
1
vote
13
replies
242
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 11 hours ago
fernanda.backsouza
▴ 10
15 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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