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ExpressionData
•
reset
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
18 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
745
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Ivan
• 0
0
votes
2
replies
1.1k
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 2.7 years ago by
pmadrigal
• 0 • written 2.7 years ago by
Kritikaverma2707
• 0
3
votes
2
replies
989
views
please resolve the issue
gene
ExpressionData
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
sonal
• 0
1
vote
2
replies
4.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 2.8 years ago by
Gordon Smyth
53k • written 2.9 years ago by
Keith
• 0
0
votes
3
replies
1.2k
views
expression data
ExpressionData
ExpressionNormalizationWorkflow
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Upasana
• 0
0
votes
0
replies
854
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR
ExpressionData
RNASeqData
3.7 years ago
Mafalda
• 0
0
votes
1
reply
1.2k
views
HSMMSingleCell metadata
ExperimentHubData
ExpressionData
CellDataSet
RNASeqData
3.7 years ago
karl.stamm
▴ 10
2
votes
2
replies
1.3k
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 3.7 years ago by
fivescarynightsgames
• 0 • written 3.8 years ago by
reza
▴ 10
0
votes
3
replies
1.3k
views
Error in loading data set
ExpressionData
updated 3.9 years ago by
Basti
▴ 780 • written 3.9 years ago by
Muhammad
• 0
0
votes
0
replies
827
views
Gene expression changes in one condition
RNASeq
Gene
ExpressionData
4.1 years ago
AZ
▴ 30
0
votes
2
replies
2.4k
views
PCA and heatmaps: most variable genes selection
DESeq2
ExpressionData
heatmaps
pca
4.5 years ago
Clara
▴ 10
3
votes
2
replies
1.7k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 4.7 years ago by
Gordon Smyth
53k • written 4.7 years ago by
Gero
• 0
1
vote
3
replies
1.4k
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
Javad_Sadeghi
• 0
0
votes
0
replies
1.8k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network
StatisticalMethod
WGCNA
ExpressionData
4.9 years ago
jol.espinoz
▴ 40
0
votes
1
reply
1.1k
views
Function createExpressionSet: Creating an ExpressionSet - Which package needed?
ExpressionData
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
Bine
▴ 50
0
votes
0
replies
1.1k
views
nested design with random factor and limma???
ExpressionData
limma
ExpressionData
limma
17.4 years ago
Gordon Smyth
53k
1
vote
0
replies
1.1k
views
nested design with random factor and limma???
ExpressionData
limma
ExpressionData
limma
17.4 years ago
Bettina Kulle Andreassen
▴ 20
0
votes
0
replies
1.4k
views
How to display or output expression data with non-unique feature labels?
ExpressionData
ExpressionData
18.5 years ago
Kocherginsky, Masha [BSD] - HSD
▴ 10
0
votes
0
replies
1.5k
views
How to display or output expression data with non-unique feature labels?
Annotation
ExpressionData
Annotation
ExpressionData
18.5 years ago
Martin Morgan
25k
20 results • Page
1 of 1
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Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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