Showing : affy • reset
1
vote
10
replies
468
views
Obtaining pheno data from CEL files
GEO affy
5 weeks ago • updated 4 weeks ago Kurtis • 0
1
vote
2
replies
233
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
6 weeks ago Mj.A. • 0
1
vote
3
replies
367
views
frma normalization
frmaTools affy
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
1
reply
621
views
affy package and SNP arrays
crlmm hapmapsnp6 genomewidesnp6Crlmm affy
updated 10 months ago by ★ 3.9k • written 10 months ago by 6.7k
2
votes
3
replies
905
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 13 months ago by ▴ 10
0
votes
3
replies
1.6k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
6
replies
2.2k
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 5 months ago by ★ 4.1k • written 17 months ago by • 0
3
votes
9
replies
2.3k
views
Installing 'affy' package on MacOS M2 chip
nlme affy preprocessCore
updated 19 months ago by 65k • written 19 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
861
views
Reading Affymetrix Axiom files
affy SNP axiom
3.0 years ago f.calboli • 0
1
vote
3
replies
970
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 3.0 years ago by 50k • written 3.0 years ago by • 0
2
votes
2
replies
989
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 ★ 3.9k • written 3.2 years ago by • 0
1
vote
2
replies
1.1k
views
Getting error in collapsing the affy probs
affy eset
updated 3.3 years ago by 65k • written 3.3 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 3.4 years ago by 65k • written 3.4 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
3.6 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
667
views
Probe Design questions
probe affy
3.6 years ago henry1995910343 • 0
0
votes
2
replies
1.1k
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
3.1k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 30
0
votes
2
replies
996
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 3.9 years ago by 50k • written 3.9 years ago by • 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 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 4.0 years ago by 65k • written 4.0 years ago by • 0
1
vote
1
reply
648
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
1.1k
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
934
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy oligo Clariom S Mouse microarray
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
0
votes
1
reply
602
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 3.9k • written 4.1 years ago by • 0
1
vote
1
reply
1.0k
views
Trouble using affy library
software error R microarray affy
updated 4.2 years ago by 65k • written 4.2 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
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 65k • written 4.5 years ago by • 0
0
votes
1
reply
873
views
limma Multi-level Experiments - Main effect test
limma microarray affy
updated 4.5 years ago by 50k • written 4.5 years ago by • 0
3
votes
2
replies
878
views
issue with hgu95acdf package
affy
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
0
votes
1
reply
942
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
994
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
1.5k
views
Using function select
Affy
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
3
votes
8
replies
2.5k
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
733
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
766
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
779
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
0
votes
0
replies
649
views
table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy insilicomerging
5.1 years ago pratikshasharma47 • 0
0
votes
0
replies
733
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 65k • written 5.1 years ago by ▴ 10
0
votes
1
reply
706
views
Differentially expressed genes in rice affymetrix data and annotation
affy microarray differentially expresed genes limma annotation
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
1
vote
1
reply
703
views
Microaaray data analysis
affy
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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