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1
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870
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HISAT2 mapping
hisat2
results
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
ali
• 0
0
votes
1
reply
3.3k
views
Heatmap with result DESeq analysis
DESeq2
results
Heatmaps
plots
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
Chiara
• 0
1
vote
2
replies
3.4k
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
3.8 years ago
james
• 0
3
votes
6
replies
2.7k
views
DESEq2 - How to extract ONE results table/coefficient from the DESeqResults object
deseq2
results
DESeqResults
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
paula.vaccarello
• 0
2
votes
2
replies
990
views
DESeq results gives all genes
deseq2
design matrix
results
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
evocanres
• 0
0
votes
1
reply
1.1k
views
Basemean always multiples of 0.5 in deseq2 results
deseq
results
baseMean
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
batmaiden
• 0
0
votes
3
replies
1.2k
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2
contrast
results
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
jan.soderman
• 0
1
vote
3
replies
1.3k
views
Results counts post DESeq same raw counts
DESeq2
results
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
A
▴ 40
0
votes
0
replies
899
views
[Questions about the results of the enrichGo()]More genes are involved but less biological activity.
enrichGO()
results
6.7 years ago
414457044
• 0
0
votes
5
replies
1.4k
views
results {DESeq2} parameters
deseq2
results
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Aurora
▴ 20
2
votes
5
replies
1.8k
views
DEGs generation parameters and specificities
deseq2
results
design and contrast matrix
updated 7.1 years ago by
Michael Love
43k • written 7.7 years ago by
tarun2
• 0
2
votes
4
replies
1.6k
views
Tac and Bioconductor giving different results
Tac
bioconductor
results
reproducbiltiy
updated 7.1 years ago by
Steve Lianoglou
★ 13k • written 7.1 years ago by
kritikamish99
▴ 10
3
votes
2
replies
3.9k
views
results(dds) error: couldn't find results. you should first run DESeq()
deseq2
results
error
7.2 years ago
hs.lansdell
▴ 20
2
votes
8
replies
1.6k
views
Deseq2 result for a variable
deseq2
differential expression
results
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
yoursbassanio
▴ 10
2
votes
5
replies
5.8k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2
results
contrast
padj
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
courtney.stairs
• 0
2
votes
5
replies
3.8k
views
Limma toptable interpretation check
limma
microarray
fdr
p-value
results
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
bhgyu
▴ 30
1
vote
6
replies
2.2k
views
DESeq2: relevel contrasts after DESeq() has been called (time-course experiment of Drosophila development)
drosophila melanogaster
multiple time points
deseq2
results
development
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
wariobrega
• 0
4
votes
4
replies
2.1k
views
Deseq2 results interpretation
deseq2
multiple factor design
results
8.6 years ago
koeniger
▴ 10
5
votes
6
replies
18k
views
Group comparison in DESeq2
deseq2
results
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
jjinhyoungkim
▴ 20
6
votes
2
replies
5.1k
views
All same padj of contrast results in the DESeq2
deseq2
padj
contrast
results
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
jjinhyoungkim
▴ 20
0
votes
3
replies
2.3k
views
Getting different results with DESeq2
deseq2
results
rstudio
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
Lillyhchen
▴ 10
5
votes
4
replies
3.7k
views
limma multiple rows per gene in output (write.fit)
limma
results
9.5 years ago
Anne
• 0
2
votes
15
replies
3.5k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.7 years ago • updated 9.6 years ago
mnaymik
▴ 10
23 results • Page
1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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