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Showing :
affy
•
reset
1
vote
10
replies
411
views
Obtaining pheno data from CEL files
GEO
affy
25 days ago • updated 18 days ago
Kurtis
• 0
1
vote
2
replies
224
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
357
views
frma normalization
frmaTools
affy
updated 9 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
michelafrancesconi8
• 0
0
votes
1
reply
594
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
879
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
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
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
848
views
Reading Affymetrix Axiom files
affy
SNP
axiom
2.9 years ago
f.calboli
• 0
1
vote
3
replies
961
views
The eBayes function gives two p-values for each row
hgu133plus2.db
limma
DifferentialExpression
affy
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Caamp
• 0
2
votes
2
replies
980
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
3.0 years ago
geoffrey
▴ 10
0
votes
1
reply
2.0k
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 3.3 years ago by
James W. MacDonald
65k • written 3.3 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
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
655
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
985
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
631
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
926
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
587
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
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 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
chziy429
• 0
0
votes
1
reply
862
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
3
votes
2
replies
872
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
925
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
981
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
726
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
759
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
769
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
0
votes
0
replies
646
views
table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy
insilicomerging
5.0 years ago
pratikshasharma47
• 0
0
votes
0
replies
728
views
How to color samples in boxplot based on treatment or control using covdesc file
affy
boxplot
5.1 years ago
pratikshasharma47
• 0
3
votes
5
replies
1.1k
views
HTA 2.0 Differential expression analysis - design question
limma
hta
affy
annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
RV
▴ 10
0
votes
1
reply
696
views
Differentially expressed genes in rice affymetrix data and annotation
affy
microarray
differentially expresed genes
limma
annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
pratikshasharma47
• 0
1
vote
1
reply
696
views
Microaaray data analysis
affy
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
p20180416
• 0
50 results • Page
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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