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Showing :
microarray
•
reset
1
vote
2
replies
2.0k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions
3factors
limma
Microarray
5.0 years ago
Dan
▴ 20
3
votes
9
replies
2.3k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
5.0 years ago • updated 4.9 years ago
Daniel.Schnell
• 0
0
votes
1
reply
1.7k
views
Creating a model matrix for three age groups using two-colour arrays
Microarray
BRAIN
Microarray
BRAIN
updated 5.0 years ago by
Gordon Smyth
53k • written 17.2 years ago by
Carthika Luxmanan
▴ 10
5
votes
8
replies
3.6k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 5.1 years ago by
James W. MacDonald
68k • written 10.5 years ago by
ben_cossins
• 0
0
votes
1
reply
1.6k
views
Normalisation of protein micro array data using VSN
microarray
normalization
protein
updated 5.2 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
keniajin
• 0
0
votes
2
replies
1.5k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
5.8 years ago • updated 5.2 years ago
Nala
• 0
0
votes
0
replies
1.8k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule
microarray
RNA-seq
WGCNA
5.3 years ago
modarzi
▴ 10
1
vote
3
replies
3.5k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray
annotation
affy
5.3 years ago
kiera.lee
▴ 10
4
votes
7
replies
2.2k
views
Limma sample groups
microarray
limma
affy
cancer
updated 5.3 years ago by
Gordon Smyth
53k • written 5.3 years ago by
nancy.nassar1590
• 0
0
votes
2
replies
1.8k
views
Regarding ArrayExpress package
microarray
arrayexpress
updated 5.3 years ago by
James W. MacDonald
68k • written 5.3 years ago by
akanksha17arora
• 0
0
votes
2
replies
1.7k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
5.3 years ago
Marco_aurelio
• 0
1
vote
6
replies
4.5k
views
TCGA: clinical data and expression data
microarray
annotation
cancer
updated 3.0 years ago by
Sharif
• 0 • written 5.4 years ago by
641549298
• 0
3
votes
1
reply
1.2k
views
Create a '.db' package for agilent
R
agilent
microarray
updated 5.4 years ago by
James W. MacDonald
68k • written 5.4 years ago by
salamandra
▴ 20
0
votes
1
reply
1.1k
views
Problem for installing arrayQualityMetrics package?
R
Microarray
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
mathavanbioinfo
▴ 20
0
votes
1
reply
913
views
Input of tscR
microarray
normalization
tscR
time-course
updated 5.5 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
keremwai
• 0
1
vote
1
reply
1.6k
views
Error in GO enrichment with topGO
topGO
microarray
Gene ontology
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
June.
▴ 10
1
vote
2
replies
1.3k
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 5.5 years ago by
Gordon Smyth
53k • written 5.5 years ago by
June.
▴ 10
2
votes
3
replies
1.9k
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray
pdInfoBuilder
oligo
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
Marton Papp
• 0
5
votes
9
replies
7.6k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray
affy
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
adR
▴ 40
0
votes
2
replies
27k
views
Installing EnhancedVolcano package in R
microarray
software error
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
kanwal.zahid.siddiqi
• 0
1
vote
1
reply
1000
views
Problem in analyzing microarray with duplicate or triplicate data
microarray
limma
5.6 years ago
peirinl
• 0
1
vote
4
replies
2.6k
views
How to compare a single RNA-Seq sample with microarray samples?
voom
rna-seq
microarray
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Sam
▴ 10
0
votes
2
replies
1.6k
views
How to process triplicate cel data?
microarray
affy
cel
drugmatrix
updated 5.6 years ago by
Gordon Smyth
53k • written 5.6 years ago by
peirinl
• 0
6
votes
3
replies
2.2k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 5.6 years ago by
Sean Davis
21k • written 5.6 years ago by
fabian
▴ 40
1
vote
2
replies
5.7k
views
Partial NA coefficients for 10 probe(s) Limma
limma
microarray
cancer
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.8 years ago by
everardoremi
• 0
0
votes
4
replies
1.9k
views
Agilent two-color microarray analysis with limma: 2x3 factorial design
limma
microarray
contrast matrix
2x3 factorial design
differential expression
updated 5.8 years ago by
Gordon Smyth
53k • written 5.8 years ago by
Natalia
• 0
0
votes
1
reply
1.5k
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy
oligo
Clariom S Mouse
microarray
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
lsbew
• 0
1
vote
5
replies
1.0k
views
Interpreting a paired limma model
limma
microarray
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
jdougherty
• 0
2
votes
4
replies
2.1k
views
After successful installation of package why it shows that Error?
software error
microarray
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
rabiulauwul
▴ 20
0
votes
1
reply
974
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma
R
microarray
timepoint
affy
updated 5.8 years ago by
shepherl
4.3k • written 5.8 years ago by
ashwinmenon1994
• 0
0
votes
0
replies
724
views
fit gene distribution to negative binomial
microarray
5.8 years ago
fabien.tell
• 0
1
vote
1
reply
1.4k
views
Trouble using affy library
software error
R
microarray
affy
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
adam_casas
• 0
1
vote
4
replies
1.7k
views
package to analyze generic protein microarray data
microarray
protein
analysis
ProteomeProfiler
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
hcnbox
• 0
2
votes
3
replies
1.8k
views
Absence of significant gene in DEG list
limma
microarray
7.8 years ago • updated 5.9 years ago
nia
▴ 20
33
votes
0
replies
45k
views
limma moderated t-statistics and B-statistics
Microarray
limma
21.3 years ago • updated 5.3 years ago
Gordon Smyth
53k
0
votes
2
replies
1.2k
views
csSAMfit with covariates
limma
microarray
deconvolution
cell type
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
antgomo
• 0
0
votes
2
replies
970
views
arrayQualityMetrics R for outlier detection
microarray
outlier detection
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
lily
▴ 20
6
votes
6
replies
6.4k
views
Finding enriched pathways from a gene list.
microarray
limma
kegg
ENTREZ
enrichment analysis
updated 5.9 years ago by
Gordon Smyth
53k • written 5.9 years ago by
omarrafiqued
▴ 50
0
votes
0
replies
1.3k
views
metaDE R and RRA R
microarray
meta analysis
5.9 years ago
lily
▴ 20
2
votes
2
replies
1.7k
views
Microarray expression analysis
microarray
normalization
CEL.gz
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
manuchandwadkar
• 0
4
votes
5
replies
2.2k
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 6.0 years ago by
Gordon Smyth
53k • written 6.0 years ago by
Pietro
▴ 40
0
votes
1
reply
919
views
normalized multiple microarrays with different design files oligo
microarray
oligo
updated 6.0 years ago by
James W. MacDonald
68k • written 6.0 years ago by
benjamin-gansemer
• 0
0
votes
2
replies
1.5k
views
gpr format microarray analysis
microarray
updated 6.0 years ago by
Robert Castelo
★ 3.4k • written 6.0 years ago by
jonathanpa12
• 0
0
votes
0
replies
3.0k
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
6.1 years ago
anne.bozack
• 0
2
votes
6
replies
5.2k
views
Convert Chromosome postions to hgnc_symbol using R
microarray
updated 3.1 years ago by
mbansal
• 0 • written 6.1 years ago by
joyk2a
• 0
0
votes
2
replies
1.9k
views
3' microarray data using Affy - can't find cdf file, please help!
Affy
microarray
cdf
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
meganlloyd
• 0
0
votes
2
replies
1.0k
views
EventPointer analysis error
microarray
EventPointer
updated 6.2 years ago by
shepherl
4.3k • written 6.2 years ago by
paulina10134
• 0
0
votes
1
reply
1.2k
views
Package not found bioconductor gCMAP
microarray
cmap
package
gCMAP
gCAMPWeb
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
bastien.chassagnol
• 0
6
votes
4
replies
3.4k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray
mirna
oligo package
pdinfobuilder
pd.mirna
updated 6.2 years ago by
soumyab.g
▴ 10 • written 8.6 years ago by
rolan.zauner
▴ 20
0
votes
1
reply
1.3k
views
limma Multi-level Experiments - Main effect test
limma
microarray
affy
updated 6.2 years ago by
Gordon Smyth
53k • written 6.2 years ago by
cyusufd
• 0
2,319 results • Page
2 of 47
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Julia Broadbent
• 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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