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deseqdataset
•
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3
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4
replies
8.2k
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DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet
DESeqDataSetFromMatrix
rnaseq
deseq2
7.8 years ago
ErickF
▴ 40
0
votes
2
replies
5.1k
views
Plots and Heat Maps not displaying in RGui Window
plot
heatmap
graphical
rnaseqgene
deseqdataset
9.0 years ago
greg.mulhearn
• 0
2
votes
10
replies
4.7k
views
DESeqDataSet 2 factors with a covariate
covariate
deseqdataset
Deseq2
multiple factor design
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
Lillyhchen
▴ 10
1
vote
4
replies
4.3k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment
deseq2
deseqdataset
multiple factor design
differential gene expression
8.7 years ago
Lillyhchen
▴ 10
2
votes
1
reply
4.0k
views
DESeq2 error when creating the DESeqDataSet
deseq2
bioconductor
deseqdataset
r
summarizedexperiment
7.5 years ago
sebastian.lobentanzer
▴ 50
3
votes
7
replies
3.8k
views
Transcript level differential expression analysis
deseq2
deseqdataset
transcripts
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
tarun2
• 0
5
votes
8
replies
3.3k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment
DESeqDataSet
GenomicRanges
DESeq2
save
updated 9.2 years ago by
Wolfgang Huber
★ 13k • written 9.2 years ago by
akaever
▴ 30
0
votes
2
replies
3.0k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2
deseqdataset
rnaseqgene
fastq
reference genome
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
greg.mulhearn
• 0
1
vote
3
replies
2.6k
views
deseq2 DESeqDataSet size when saved
deseq2
infrastructure
deseqdataset
importing
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
eric.blanc
• 0
1
vote
2
replies
1.3k
views
DESeq2: different number of significant genes between DESeqDataSetFromMatrix and DESeqDataSetFromHTSeqCount
deseq2
deseqdatasetfrommatrix
deseqdataset
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
jillian.waters
• 0
0
votes
2
replies
961
views
Error when creating a DESeqDataSet object
deseq2
DESeqDataSet
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
colaneri
▴ 30
0
votes
2
replies
886
views
constructing a DESeqDataSet
deseq2
DESeqDataSet
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
linouhao
▴ 20
12 results • Page
1 of 1
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Replies
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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