Showing : affy • reset
2
votes
3
replies
263
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 7 weeks ago by 63k • written 7 weeks ago by ▴ 10
0
votes
3
replies
240
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 9 weeks ago by 63k • written 10 weeks ago by • 0
0
votes
1
reply
991
views
limma: decideTests
affy limma affy limma
updated 4 months ago by 47k • written 15.5 years ago by ▴ 270
0
votes
4
replies
868
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 5 months ago by ▴ 70 • written 6 months ago by • 0
3
votes
9
replies
1.2k
views
Installing 'affy' package on MacOS M2 chip
nlme affy preprocessCore
updated 7 months ago by 63k • written 8 months ago by • 0
1
vote
3
replies
726
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 20 months ago by 63k • written 20 months ago by • 0
0
votes
0
replies
551
views
Reading Affymetrix Axiom files
affy SNP axiom
2.1 years ago f.calboli • 0
1
vote
3
replies
641
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 2.1 years ago by 47k • written 2.1 years ago by • 0
2
votes
2
replies
661
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
2.1 years ago geoffrey ▴ 10
0
votes
1
reply
1.1k
views
filtering on variance
probe affy probe affy
updated 2.1 years ago by 47k • written 15.5 years ago by ▴ 90
0
votes
1
reply
1.2k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 2.3 years ago by 3.8k • written 2.3 years ago by • 0
1
vote
2
replies
713
views
Getting error in collapsing the affy probs
affy eset
updated 2.4 years ago by 63k • written 2.4 years ago by ▴ 30
0
votes
3
replies
911
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 2.5 years ago by 63k • written 2.5 years ago by • 0
5
votes
8
replies
2.0k
views
how to annotate arrays
affy annotation microarray oligo
updated 2.5 years ago by 63k • written 7.9 years ago by • 0
1
vote
3
replies
1.8k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray annotation affy
2.7 years ago kiera.lee ▴ 10
4
votes
7
replies
982
views
Limma sample groups
microarray limma affy cancer
updated 2.7 years ago by 47k • written 2.7 years ago by • 0
0
votes
0
replies
382
views
Probe Design questions
probe affy
2.7 years ago henry1995910343 • 0
0
votes
2
replies
737
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
2.7 years ago Marco_aurelio • 0
0
votes
6
replies
706
views
Problems loading latest Version of S4Vectors
affy
2.8 years ago ianrector97 • 0
5
votes
9
replies
1.9k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 3.0 years ago by 3.8k • written 3.0 years ago by ▴ 30
0
votes
2
replies
648
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
6
votes
3
replies
902
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 40
2
votes
7
replies
772
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
1
vote
1
reply
385
views
Microarray Workflow - NA error
limma affy
updated 3.1 years ago by 3.8k • written 3.1 years ago by • 0
3
votes
4
replies
637
views
gcrma problem with make.cdf.package
gcrma make.cdf.package affy
updated 3.1 years ago by 63k • written 3.1 years ago by ▴ 40
0
votes
1
reply
625
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 3.1 years ago by 63k • written 3.1 years ago by • 0
0
votes
1
reply
369
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma R microarray timepoint affy
updated 3.2 years ago by 3.5k • written 3.2 years ago by • 0
1
vote
1
reply
730
views
Trouble using affy library
software error R microarray affy
updated 3.2 years ago by 63k • written 3.2 years ago by • 0
1
vote
1
reply
1.1k
views
How to annotate the Affymetrix data HTA-2.0 with oligo
annotation affy normalization
updated 3.3 years ago by ★ 3.6k • written 3.3 years ago by • 0
0
votes
2
replies
902
views
3' microarray data using Affy - can't find cdf file, please help!
Affy microarray cdf
updated 3.5 years ago by 63k • written 3.5 years ago by • 0
0
votes
1
reply
568
views
limma Multi-level Experiments - Main effect test
limma microarray affy
updated 3.6 years ago by 47k • written 3.6 years ago by • 0
0
votes
2
replies
706
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy rma frma oligo
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
3
votes
2
replies
549
views
issue with hgu95acdf package
affy
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
0
votes
1
reply
589
views
Still Not Recognizing CDF
affy CDF
3.6 years ago ekl • 0
1
vote
5
replies
1.2k
views
CDf files in R
affy CDF
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
1
vote
2
replies
612
views
What should I do with the package:org.Hs.eg.db?
microarray affy
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 10
2
votes
4
replies
928
views
Using function select
Affy
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
3
votes
8
replies
1.9k
views
Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy limma piano
updated 3.7 years ago by 63k • written 3.7 years ago by • 0
0
votes
0
replies
519
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray affy rma normalization affy package
3.8 years ago yshuang • 0
1
vote
2
replies
1.5k
views
CDF not found
Affy microarray
updated 3.8 years ago by ★ 3.6k • written 3.8 years ago by ▴ 10
0
votes
0
replies
558
views
Fold Change Calculation in edge package
edge microarray limma affy
4.0 years ago soumyab.g ▴ 10
6
votes
8
replies
1.2k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
4.0 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
489
views
"hgu133plus2db" package not working in R
microarray affy annotation
updated 4.0 years ago by 63k • written 4.0 years ago by • 0
2
votes
8
replies
973
views
affycoretools package, HTA 2.0 annotation query
annotation affy
updated 4.1 years ago by 63k • written 4.1 years ago by ▴ 10
0
votes
0
replies
469
views
table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy insilicomerging
4.2 years ago pratikshasharma47 • 0
0
votes
0
replies
520
views
How to color samples in boxplot based on treatment or control using covdesc file
affy boxplot
4.2 years ago pratikshasharma47 • 0
3
votes
5
replies
766
views
HTA 2.0 Differential expression analysis - design question
limma hta affy annotation
updated 4.2 years ago by 63k • written 4.2 years ago by ▴ 10
0
votes
1
reply
523
views
Differentially expressed genes in rice affymetrix data and annotation
affy microarray differentially expresed genes limma annotation
updated 4.2 years ago by 63k • written 4.2 years ago by • 0
1
vote
1
reply
490
views
Microaaray data analysis
affy
updated 4.2 years ago by 63k • written 4.2 years ago by • 0
0
votes
0
replies
484
views
fData slot in gene expression analysis
affy microarray gene expression analysis
4.2 years ago pratikshasharma47 • 0
50 results • Page 1 of 1
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Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
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