Showing : affy • reset
0
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3
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1.3k
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How to analyze Affy data, CEL files not available
affy affy
written 19.0 years ago by ▴ 60
1
vote
2
replies
726
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
1.6k
views
ERROR; return code from pthread_create() is 22
affy
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
10
replies
2.1k
views
Obtaining pheno data from CEL files
GEO affy
21 months ago Kurtis • 0
1
vote
2
replies
802
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
22 months ago Mj.A. ▴ 20
1
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3
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1.0k
views
frma normalization
frmaTools affy
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
11
replies
3.1k
views
globaltest question
Pathways probe affy Pathways probe affy
written 19.4 years ago by ▴ 30
0
votes
5
replies
2.8k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 12.0 years ago by ★ 13k
0
votes
6
replies
3.7k
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 2.2 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
votes
1
reply
1.2k
views
affy package and SNP arrays
crlmm hapmapsnp6 genomewidesnp6Crlmm affy
updated 2.6 years ago by ★ 4.0k • written 2.6 years ago by 6.7k
2
votes
3
replies
1.6k
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 10
0
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3
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3.8k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
1
reply
1.7k
views
limma: decideTests
affy limma affy limma
updated 3.0 years ago by 53k • written 18.1 years ago by ▴ 270
3
votes
9
replies
3.6k
views
Installing 'affy' package on MacOS M2 chip
nlme affy preprocessCore
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
1
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3
replies
1.8k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
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0
replies
1.5k
views
Reading Affymetrix Axiom files
affy SNP axiom
4.7 years ago f.calboli • 0
1
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3
replies
1.5k
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 4.7 years ago by 53k • written 4.7 years ago by • 0
2
votes
2
replies
1.5k
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
4.7 years ago geoffrey ▴ 10
0
votes
1
reply
1.9k
views
filtering on variance
probe affy probe affy
updated 4.7 years ago by 53k • written 18.1 years ago by ▴ 90
0
votes
1
reply
3.4k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
1
vote
2
replies
1.8k
views
Getting error in collapsing the affy probs
affy eset
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
0
votes
3
replies
2.1k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
5
votes
8
replies
3.6k
views
how to annotate arrays
affy annotation microarray oligo
updated 5.1 years ago by 68k • written 10.5 years ago by • 0
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 53k • written 5.3 years ago by • 0
0
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0
replies
1.1k
views
Probe Design questions
probe affy
5.3 years ago henry1995910343 • 0
0
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2
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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
0
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6
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1.7k
views
Problems loading latest Version of S4Vectors
affy
5.4 years ago ianrector97 • 0
5
votes
9
replies
7.5k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 40
0
votes
2
replies
1.6k
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 5.6 years ago by 53k • written 5.6 years ago by • 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 21k • written 5.6 years ago by ▴ 40
2
votes
7
replies
1.9k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
1
reply
1.0k
views
Microarray Workflow - NA error
limma affy
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
3
votes
4
replies
1.6k
views
gcrma problem with make.cdf.package
gcrma make.cdf.package affy
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 40
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 68k • written 5.8 years ago by • 0
0
votes
1
reply
971
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 4.3k • written 5.8 years ago by • 0
1
vote
1
reply
1.4k
views
Trouble using affy library
software error R microarray affy
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
1
vote
1
reply
2.6k
views
How to annotate the Affymetrix data HTA-2.0 with oligo
annotation affy normalization
updated 5.9 years ago by ★ 4.1k • written 5.9 years ago by • 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 68k • written 6.1 years ago by • 0
0
votes
1
reply
1.3k
views
limma Multi-level Experiments - Main effect test
limma microarray affy
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
0
votes
2
replies
1.7k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy rma frma oligo
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
3
votes
2
replies
1.3k
views
issue with hgu95acdf package
affy
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
1
reply
1.4k
views
Still Not Recognizing CDF
affy CDF
6.2 years ago ekl • 0
1
vote
5
replies
2.7k
views
CDf files in R
affy CDF
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
1
vote
2
replies
1.7k
views
What should I do with the package:org.Hs.eg.db?
microarray affy
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 10
2
votes
4
replies
2.3k
views
Using function select
Affy
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
3
votes
8
replies
4.0k
views
Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy limma piano
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
0
votes
0
replies
1.1k
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray affy rma normalization affy package
6.4 years ago yshuang • 0
1
vote
2
replies
3.0k
views
CDF not found
Affy microarray
updated 6.4 years ago by ★ 4.1k • written 6.4 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Fold Change Calculation in edge package
edge microarray limma affy
6.6 years ago soumyab.g ▴ 10
1,805 results • Page 1 of 37
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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