Showing : microarray • reset
3
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9
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2.1k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.6 years ago Daniel.Schnell • 0
0
votes
1
reply
1.6k
views
Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 4.6 years ago by 53k • written 16.8 years ago by ▴ 10
5
votes
8
replies
3.4k
views
how to annotate arrays
affy annotation microarray oligo
updated 4.8 years ago by 68k • written 10.1 years ago by • 0
0
votes
1
reply
1.4k
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 4.8 years ago by ★ 13k • written 6.2 years ago by • 0
0
votes
2
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1.4k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
5.4 years ago • updated 4.9 years ago Nala • 0
0
votes
0
replies
1.6k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
4.9 years ago modarzi ▴ 10
1
vote
3
replies
3.3k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray annotation affy
4.9 years ago kiera.lee ▴ 10
4
votes
7
replies
2.0k
views
Limma sample groups
microarray limma affy cancer
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
0
votes
2
replies
1.7k
views
Regarding ArrayExpress package
microarray arrayexpress
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
votes
2
replies
1.5k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
5.0 years ago Marco_aurelio • 0
1
vote
6
replies
4.0k
views
TCGA: clinical data and expression data
microarray annotation cancer
updated 2.6 years ago by • 0 • written 5.0 years ago by • 0
3
votes
1
reply
1.1k
views
Create a '.db' package for agilent
R agilent microarray
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
0
votes
1
reply
1.0k
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 20
0
votes
1
reply
822
views
Input of tscR
microarray normalization tscR time-course
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
1
vote
1
reply
1.5k
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 5.1 years ago by 68k • written 5.2 years ago by ▴ 10
1
vote
2
replies
1.2k
views
How to construct matrix and fit linear model for this microarray?
microarray dge matrix makecontrasts limma
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 10
2
votes
3
replies
1.8k
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray pdInfoBuilder oligo
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
5
votes
9
replies
6.2k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 40
0
votes
2
replies
27k
views
Installing EnhancedVolcano package in R
microarray software error
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
1
vote
1
reply
927
views
Problem in analyzing microarray with duplicate or triplicate data
microarray limma
5.2 years ago peirinl • 0
1
vote
4
replies
2.3k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
6
votes
3
replies
2.0k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 40
1
vote
2
replies
5.5k
views
Partial NA coefficients for 10 probe(s) Limma
limma microarray cancer
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
4
replies
1.8k
views
Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 5.4 years ago by 53k • written 5.5 years ago by • 0
0
votes
1
reply
1.4k
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
vote
5
replies
881
views
Interpreting a paired limma model
limma microarray
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
2
votes
4
replies
2.0k
views
After successful installation of package why it shows that Error?
software error microarray
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
0
votes
1
reply
890
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma R microarray timepoint affy
updated 5.4 years ago by 4.2k • written 5.4 years ago by • 0
0
votes
0
replies
660
views
fit gene distribution to negative binomial
microarray
5.5 years ago fabien.tell • 0
1
vote
1
reply
1.3k
views
Trouble using affy library
software error R microarray affy
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
1
vote
4
replies
1.5k
views
package to analyze generic protein microarray data
microarray protein analysis ProteomeProfiler
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
2
votes
3
replies
1.6k
views
Absence of significant gene in DEG list
limma microarray
7.4 years ago • updated 5.5 years ago nia ▴ 30
32
votes
0
replies
44k
views
limma moderated t-statistics and B-statistics
Microarray limma
21.0 years ago • updated 4.9 years ago Gordon Smyth 53k
0
votes
2
replies
1.1k
views
csSAMfit with covariates
limma microarray deconvolution cell type
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
votes
2
replies
905
views
arrayQualityMetrics R for outlier detection
microarray outlier detection
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 20
6
votes
6
replies
6.1k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 50
0
votes
0
replies
1.2k
views
metaDE R and RRA R
microarray meta analysis
5.6 years ago lily ▴ 20
2
votes
2
replies
1.6k
views
Microarray expression analysis
microarray normalization CEL.gz
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
4
votes
5
replies
2.0k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 40
0
votes
1
reply
842
views
normalized multiple microarrays with different design files oligo
microarray oligo
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
2
replies
1.4k
views
gpr format microarray analysis
microarray
updated 5.7 years ago by ★ 3.4k • written 5.7 years ago by • 0
0
votes
0
replies
2.8k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.7 years ago anne.bozack • 0
2
votes
6
replies
5.0k
views
Convert Chromosome postions to hgnc_symbol using R
microarray
updated 2.7 years ago by • 0 • written 5.8 years ago by • 0
0
votes
2
replies
1.8k
views
3' microarray data using Affy - can't find cdf file, please help!
Affy microarray cdf
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
2
replies
946
views
EventPointer analysis error
microarray EventPointer
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
Package not found bioconductor gCMAP
microarray cmap package gCMAP gCAMPWeb
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
6
votes
4
replies
3.3k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray mirna oligo package pdinfobuilder pd.mirna
updated 5.8 years ago by ▴ 10 • written 8.3 years ago by ▴ 20
0
votes
1
reply
1.2k
views
limma Multi-level Experiments - Main effect test
limma microarray affy
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
0
votes
2
replies
1.3k
views
Longitudinal Time-Course microarray experiment with two time points
edge DGE microarray
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
2,319 results • Page 2 of 47
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Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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