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Showing :
ExpressionData
•
reset
3
votes
2
replies
779
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
9 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
552
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 22 months ago by
Michael Love
43k • written 22 months ago by
Ivan
• 0
0
votes
2
replies
858
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 23 months ago by
pmadrigal
• 0 • written 23 months ago by
Kritikaverma2707
• 0
3
votes
2
replies
784
views
please resolve the issue
gene
ExpressionData
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
sonal
• 0
1
vote
2
replies
3.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Keith
• 0
0
votes
3
replies
1.0k
views
expression data
ExpressionData
ExpressionNormalizationWorkflow
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Upasana
• 0
0
votes
0
replies
721
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR
ExpressionData
RNASeqData
2.9 years ago
Mafalda
• 0
0
votes
1
reply
925
views
HSMMSingleCell metadata
ExperimentHubData
ExpressionData
CellDataSet
RNASeqData
2.9 years ago
karl.stamm
▴ 10
2
votes
2
replies
1.1k
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 2.9 years ago by
fivescarynightsgames
• 0 • written 3.0 years ago by
reza
▴ 10
0
votes
3
replies
1.1k
views
Error in loading data set
ExpressionData
updated 3.1 years ago by
Basti
▴ 780 • written 3.1 years ago by
Muhammad
• 0
0
votes
0
replies
684
views
Gene expression changes in one condition
RNASeq
Gene
ExpressionData
3.3 years ago
AZ
▴ 30
0
votes
2
replies
2.1k
views
PCA and heatmaps: most variable genes selection
DESeq2
ExpressionData
heatmaps
pca
3.7 years ago
Clara
▴ 10
3
votes
2
replies
1.4k
views
NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData
ArrayExpress
updated 3.9 years ago by
Gordon Smyth
52k • written 3.9 years ago by
Gero
• 0
1
vote
3
replies
1.2k
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
Javad_Sadeghi
• 0
0
votes
0
replies
1.5k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network
StatisticalMethod
WGCNA
ExpressionData
4.1 years ago
jol.espinoz
▴ 40
0
votes
1
reply
895
views
Function createExpressionSet: Creating an ExpressionSet - Which package needed?
ExpressionData
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
Bine
▴ 50
0
votes
0
replies
956
views
nested design with random factor and limma???
ExpressionData
limma
ExpressionData
limma
16.6 years ago
Gordon Smyth
52k
1
vote
0
replies
953
views
nested design with random factor and limma???
ExpressionData
limma
ExpressionData
limma
16.6 years ago
Bettina Kulle Andreassen
▴ 20
0
votes
0
replies
1.2k
views
How to display or output expression data with non-unique feature labels?
ExpressionData
ExpressionData
17.7 years ago
Kocherginsky, Masha [BSD] - HSD
▴ 10
0
votes
0
replies
1.4k
views
How to display or output expression data with non-unique feature labels?
Annotation
ExpressionData
Annotation
ExpressionData
17.7 years ago
Martin Morgan
25k
20 results • Page
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Replies
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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