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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
741
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
984
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
847
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 3.7 years ago by
reza
▴ 10
0
votes
3
replies
1.3k
views
Error in loading data set
ExpressionData
updated 3.8 years ago by
Basti
▴ 780 • written 3.8 years ago by
Muhammad
• 0
0
votes
0
replies
820
views
Gene expression changes in one condition
RNASeq
Gene
ExpressionData
4.0 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 4.6 years ago by
Gordon Smyth
53k • written 4.6 years ago by
Gero
• 0
1
vote
3
replies
1.4k
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 4.8 years ago by
Michael Love
43k • written 4.8 years ago by
Javad_Sadeghi
• 0
0
votes
0
replies
1.7k
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
18.4 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
18.4 years ago
Martin Morgan
25k
20 results • Page
1 of 1
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Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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