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HISAT2 mapping
hisat2
results
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
ali
• 0
0
votes
1
reply
2.1k
views
Heatmap with result DESeq analysis
DESeq2
results
Heatmaps
plots
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Chiara
• 0
1
vote
2
replies
2.9k
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
3.2 years ago
james
• 0
3
votes
6
replies
2.3k
views
DESEq2 - How to extract ONE results table/coefficient from the DESeqResults object
deseq2
results
DESeqResults
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
paula.vaccarello
• 0
2
votes
2
replies
813
views
DESeq results gives all genes
deseq2
design matrix
results
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
evocanres
• 0
0
votes
1
reply
900
views
Basemean always multiples of 0.5 in deseq2 results
deseq
results
baseMean
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
batmaiden
• 0
0
votes
3
replies
1.0k
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2
contrast
results
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
jan.soderman
• 0
1
vote
3
replies
1.0k
views
Results counts post DESeq same raw counts
DESeq2
results
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
A
▴ 40
0
votes
0
replies
767
views
[Questions about the results of the enrichGo()]More genes are involved but less biological activity.
enrichGO()
results
6.1 years ago
414457044
• 0
0
votes
5
replies
1.2k
views
results {DESeq2} parameters
deseq2
results
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
Aurora
▴ 20
2
votes
4
replies
1.3k
views
Tac and Bioconductor giving different results
Tac
bioconductor
results
reproducbiltiy
updated 6.5 years ago by
Steve Lianoglou
★ 13k • written 6.5 years ago by
kritikamish99
▴ 10
3
votes
2
replies
3.3k
views
results(dds) error: couldn't find results. you should first run DESeq()
deseq2
results
error
6.5 years ago
hs.lansdell
▴ 20
2
votes
8
replies
1.3k
views
Deseq2 result for a variable
deseq2
differential expression
results
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
yoursbassanio
▴ 10
2
votes
5
replies
5.2k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2
results
contrast
padj
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
courtney.stairs
• 0
2
votes
5
replies
3.2k
views
Limma toptable interpretation check
limma
microarray
fdr
p-value
results
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
bhgyu
▴ 30
2
votes
5
replies
1.5k
views
DEGs generation parameters and specificities
deseq2
results
design and contrast matrix
updated 6.5 years ago by
Michael Love
41k • written 7.0 years ago by
tarun2
• 0
1
vote
6
replies
1.9k
views
DESeq2: relevel contrasts after DESeq() has been called (time-course experiment of Drosophila development)
drosophila melanogaster
multiple time points
deseq2
results
development
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
wariobrega
• 0
4
votes
4
replies
1.8k
views
Deseq2 results interpretation
deseq2
multiple factor design
results
7.9 years ago
koeniger
▴ 10
5
votes
6
replies
18k
views
Group comparison in DESeq2
deseq2
results
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
jjinhyoungkim
▴ 20
6
votes
2
replies
4.8k
views
All same padj of contrast results in the DESeq2
deseq2
padj
contrast
results
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
jjinhyoungkim
▴ 20
0
votes
3
replies
2.1k
views
Getting different results with DESeq2
deseq2
results
rstudio
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
Lillyhchen
▴ 10
5
votes
4
replies
3.5k
views
limma multiple rows per gene in output (write.fit)
limma
results
8.9 years ago
Anne
• 0
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.1 years ago • updated 9.0 years ago
mnaymik
▴ 10
23 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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