Showing : affy • reset
1
vote
10
replies
378
views
Obtaining pheno data from CEL files
GEO affy
16 days ago • updated 9 days ago Kurtis • 0
1
vote
2
replies
207
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
23 days ago Mj.A. • 0
1
vote
3
replies
347
views
frma normalization
frmaTools affy
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.6 years ago by ▴ 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 ★ 13k
0
votes
6
replies
2.1k
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 5 months ago by ★ 4.0k • written 16 months ago by • 0
0
votes
1
reply
575
views
affy package and SNP arrays
crlmm hapmapsnp6 genomewidesnp6Crlmm affy
updated 9 months ago by ★ 3.9k • written 9 months ago by 6.7k
2
votes
3
replies
865
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 65k • written 12 months ago by ▴ 10
0
votes
3
replies
1.5k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
1
reply
1.3k
views
limma: decideTests
affy limma affy limma
updated 14 months ago by 50k • written 16.3 years ago by ▴ 270
3
votes
9
replies
2.3k
views
Installing 'affy' package on MacOS M2 chip
nlme affy preprocessCore
updated 18 months ago by 65k • written 18 months ago by • 0
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
0
votes
0
replies
835
views
Reading Affymetrix Axiom files
affy SNP axiom
2.9 years ago f.calboli • 0
1
vote
3
replies
950
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
2
votes
2
replies
969
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
2.9 years ago geoffrey ▴ 10
0
votes
1
reply
1.4k
views
filtering on variance
probe affy probe affy
updated 3.0 years ago by 50k • written 16.4 years ago by ▴ 90
0
votes
1
reply
1.9k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
2
replies
1.0k
views
Getting error in collapsing the affy probs
affy eset
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 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 65k • written 3.3 years ago by • 0
5
votes
8
replies
2.5k
views
how to annotate arrays
affy annotation microarray oligo
updated 3.4 years ago by 65k • written 8.7 years ago by • 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 50k • written 3.6 years ago by • 0
0
votes
0
replies
635
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
1.0k
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 ★ 3.9k • written 3.8 years ago by ▴ 30
0
votes
2
replies
976
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
6
votes
3
replies
1.3k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 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 65k • written 3.9 years ago by • 0
1
vote
1
reply
615
views
Microarray Workflow - NA error
limma affy
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 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 65k • written 4.0 years ago by ▴ 40
0
votes
1
reply
909
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
0
votes
1
reply
576
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 3.8k • written 4.1 years ago by • 0
1
vote
1
reply
1.0k
views
Trouble using affy library
software error R microarray affy
updated 4.1 years ago by 65k • written 4.1 years ago by • 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 ★ 3.9k • written 4.2 years ago by • 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 65k • written 4.4 years ago by • 0
0
votes
1
reply
853
views
limma Multi-level Experiments - Main effect test
limma microarray affy
updated 4.4 years ago by 50k • written 4.4 years ago by • 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 65k • written 4.4 years ago by • 0
3
votes
2
replies
859
views
issue with hgu95acdf package
affy
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
0
votes
1
reply
913
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 65k • written 4.5 years ago by • 0
1
vote
2
replies
967
views
What should I do with the package:org.Hs.eg.db?
microarray affy
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
2
votes
4
replies
1.4k
views
Using function select
Affy
updated 4.5 years ago by 65k • written 4.5 years ago by • 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 65k • written 4.6 years ago by • 0
0
votes
0
replies
716
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 ★ 3.9k • written 4.7 years ago by ▴ 10
0
votes
0
replies
748
views
Fold Change Calculation in edge package
edge microarray limma affy
4.8 years ago soumyab.g ▴ 10
6
votes
8
replies
1.7k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
4.8 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
760
views
"hgu133plus2db" package not working in R
microarray affy annotation
updated 4.9 years ago by 65k • written 4.9 years ago by • 0
2
votes
8
replies
1.4k
views
affycoretools package, HTA 2.0 annotation query
annotation affy
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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