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Showing :
affy
•
reset
1
vote
10
replies
406
views
Obtaining pheno data from CEL files
GEO
affy
23 days ago • updated 17 days ago
Kurtis
• 0
1
vote
2
replies
220
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
4 weeks ago
Mj.A.
• 0
1
vote
3
replies
354
views
frma normalization
frmaTools
affy
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
michelafrancesconi8
• 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.6 years ago by
mike Ad.
▴ 30
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation
affy
oligo
ffpe
Annotation
affy
oligo
ffpe
written 10.3 years ago by
Guest User
★ 13k
0
votes
6
replies
2.1k
views
Error when Installing BioConductor Package ('affy')
Bioconductor
Install
affy
updated 5 months ago by
ATpoint
★ 4.0k • written 17 months ago by
laujihen
• 0
0
votes
1
reply
588
views
affy package and SNP arrays
crlmm
hapmapsnp6
genomewidesnp6Crlmm
affy
updated 10 months ago by
Kevin Blighe
★ 3.9k • written 10 months ago by
Vincent J. Carey, Jr.
6.7k
2
votes
3
replies
878
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 12 months ago by
James W. MacDonald
65k • written 12 months ago by
Pratik Mehta
▴ 10
0
votes
3
replies
1.5k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools
FRMA
affyio
AffymetrixDataTestFiles
affy
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Seymoo
• 0
0
votes
1
reply
1.3k
views
limma: decideTests
affy
limma
affy
limma
updated 15 months ago by
Gordon Smyth
50k • written 16.4 years ago by
Al Ivens
▴ 270
3
votes
9
replies
2.3k
views
Installing 'affy' package on MacOS M2 chip
nlme
affy
preprocessCore
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
albrecht5698
• 0
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
RMP87
• 0
0
votes
0
replies
847
views
Reading Affymetrix Axiom files
affy
SNP
axiom
2.9 years ago
f.calboli
• 0
1
vote
3
replies
960
views
The eBayes function gives two p-values for each row
hgu133plus2.db
limma
DifferentialExpression
affy
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Caamp
• 0
2
votes
2
replies
978
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
3.0 years ago
geoffrey
▴ 10
0
votes
1
reply
1.4k
views
filtering on variance
probe
affy
probe
affy
updated 3.0 years ago by
Gordon Smyth
50k • written 16.4 years ago by
Dennis.Burian@faa.gov
▴ 90
0
votes
1
reply
1.9k
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Lara
• 0
1
vote
2
replies
1.1k
views
Getting error in collapsing the affy probs
affy
eset
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
AZ
▴ 30
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 3.3 years ago by
James W. MacDonald
65k • written 3.4 years ago by
bastien_chassagnol
• 0
5
votes
8
replies
2.5k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 3.4 years ago by
James W. MacDonald
65k • written 8.7 years ago by
ben_cossins
• 0
1
vote
3
replies
2.4k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray
annotation
affy
3.5 years ago
kiera.lee
▴ 10
4
votes
7
replies
1.5k
views
Limma sample groups
microarray
limma
affy
cancer
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
nancy.nassar1590
• 0
0
votes
0
replies
651
views
Probe Design questions
probe
affy
3.6 years ago
henry1995910343
• 0
0
votes
2
replies
1.0k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
3.6 years ago
Marco_aurelio
• 0
0
votes
6
replies
1.1k
views
Problems loading latest Version of S4Vectors
affy
3.7 years ago
ianrector97
• 0
5
votes
9
replies
3.0k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray
affy
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
adR
▴ 30
0
votes
2
replies
984
views
How to process triplicate cel data?
microarray
affy
cel
drugmatrix
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
peirinl
• 0
6
votes
3
replies
1.4k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 3.9 years ago by
Sean Davis
21k • written 3.9 years ago by
fabian
▴ 40
2
votes
7
replies
1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Marco_aurelio
• 0
1
vote
1
reply
628
views
Microarray Workflow - NA error
limma
affy
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
ammasakshay
• 0
3
votes
4
replies
1.0k
views
gcrma problem with make.cdf.package
gcrma
make.cdf.package
affy
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Osvaldo
▴ 40
0
votes
1
reply
920
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy
oligo
Clariom S Mouse
microarray
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
lsbew
• 0
0
votes
1
reply
585
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma
R
microarray
timepoint
affy
updated 4.1 years ago by
shepherl
3.8k • written 4.1 years ago by
ashwinmenon1994
• 0
1
vote
1
reply
1.0k
views
Trouble using affy library
software error
R
microarray
affy
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
adam_casas
• 0
1
vote
1
reply
1.7k
views
How to annotate the Affymetrix data HTA-2.0 with oligo
annotation
affy
normalization
updated 4.2 years ago by
Guido Hooiveld
★ 3.9k • written 4.2 years ago by
sheikhbeigali
• 0
0
votes
2
replies
1.3k
views
3' microarray data using Affy - can't find cdf file, please help!
Affy
microarray
cdf
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
meganlloyd
• 0
0
votes
1
reply
860
views
limma Multi-level Experiments - Main effect test
limma
microarray
affy
updated 4.4 years ago by
Gordon Smyth
50k • written 4.5 years ago by
cyusufd
• 0
0
votes
2
replies
1.0k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy
rma
frma
oligo
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
chziy429
• 0
3
votes
2
replies
871
views
issue with hgu95acdf package
affy
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
alisher.jannyyev
• 0
0
votes
1
reply
920
views
Still Not Recognizing CDF
affy
CDF
4.5 years ago
ekl
• 0
1
vote
5
replies
1.7k
views
CDf files in R
affy
CDF
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
ekl
• 0
1
vote
2
replies
978
views
What should I do with the package:org.Hs.eg.db?
microarray
affy
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
2426986765
▴ 10
2
votes
4
replies
1.5k
views
Using function select
Affy
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
ekl
• 0
3
votes
8
replies
2.4k
views
Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy
limma
piano
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
abolfazl.nikakhtar
• 0
0
votes
0
replies
722
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray
affy
rma normalization
affy package
4.7 years ago
yshuang
• 0
1
vote
2
replies
2.0k
views
CDF not found
Affy
microarray
updated 4.7 years ago by
Guido Hooiveld
★ 3.9k • written 4.7 years ago by
ijvechetti
▴ 10
0
votes
0
replies
757
views
Fold Change Calculation in edge package
edge
microarray
limma
affy
4.9 years ago
soumyab.g
▴ 10
6
votes
8
replies
1.8k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma
microarray
affy
edger
4.9 years ago
Jurat Shahidin
▴ 80
1
vote
2
replies
765
views
"hgu133plus2db" package not working in R
microarray
affy
annotation
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
rgeysels
• 0
2
votes
8
replies
1.4k
views
affycoretools package, HTA 2.0 annotation query
annotation
affy
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
a.karanikolou
▴ 10
50 results • Page
1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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