Showing : affymetrix microarrays • reset
1
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34
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6.6k
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how to check which probesets belong to which transcript?
xps affymetrix microarrays humangene2.0ST micro array data
updated 9.9 years ago by ★ 3.9k • written 9.9 years ago by ▴ 120
12
votes
20
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3.1k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 10.5 years ago by ★ 29k • written 10.5 years ago by ▴ 840
11
votes
16
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2.6k
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Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 840
10
votes
13
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5.6k
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Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 10.6 years ago by • 0 • written 10.7 years ago by ▴ 10
2
votes
10
replies
4.0k
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matching probes to genes from pd.porgene.1.1.st array
pd.porgene.1.1.st affymetrix microarrays
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 60
1
vote
8
replies
11k
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"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
10.6 years ago Claudia ▴ 10
4
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8
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2.5k
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Annotation Problem regarding double platform merged microarray eset using the inSilicoMerging R package, after differential expression analysis
inSilicoMerging doubleannotation affymetrix microarrays limma inSilicoDB
10.5 years ago svlachavas ▴ 840
4
votes
7
replies
2.8k
views
Understanding the output of the exprs() function
affymetrix microarrays
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
4
votes
7
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2.5k
views
Downloading microarray data for DEG analysis!
affymetrix microarrays
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 10
1
vote
6
replies
2.6k
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Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 8.7 years ago by ★ 13k • written 8.8 years ago by • 0
3
votes
6
replies
3.9k
views
WGCNA normalized CDF to use, WGCNA Intramodular connectivity
wgcna affymetrix microarrays affy
updated 10.6 years ago by ★ 3.0k • written 10.7 years ago by ▴ 30
12
votes
6
replies
2.1k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
1
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6
replies
3.1k
views
How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 7.9 years ago by ★ 4.1k • written 7.9 years ago by ▴ 260
1
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5
replies
2.9k
views
Removing batch effect from microarray data
removebatcheffect() microarray affymetrix microarrays
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 40
0
votes
4
replies
2.0k
views
contrast matrix design for a comparison (trend) of drug concentrations
limma contrast matrix affymetrix microarrays limma
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 840
5
votes
4
replies
4.4k
views
How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
8.2 years ago rahil ▴ 30
3
votes
4
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1.9k
views
Problem regarding the explanation of log-fold changes of individual coefficients in limma after eBayes
limma logfoldchange limma design matrix paired samples affymetrix microarrays
updated 10.4 years ago by ★ 7.9k • written 10.4 years ago by ▴ 840
1
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4
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2.1k
views
How to extract common genes that are DE in each comparisons?
limma bioconductor affymetrix microarrays R
9.1 years ago rkp • 0
3
votes
4
replies
2.0k
views
Different annotation obtained from hgu133a2.db and affymetrix annotation release
annotation hgu133plus2.db affymetrix microarrays micorarray
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 60
2
votes
4
replies
2.4k
views
Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
expressionset limma annotation affymetrix microarrays
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 840
1
vote
3
replies
1.8k
views
Limma: model Design matrix and contrast matrix for getting gene log2 fold change data
bioconductor affymetrix microarrays differential gene expression design and contrast matrix
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
4
votes
3
replies
1.7k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
1
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3
replies
2.0k
views
How to normalize Microarray expression data?
r affymetrix microarrays normalization bioconductor
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 120
2
votes
3
replies
1.8k
views
How to create vectors (makeVectorsAffyBatch) , using own cdf
affymetrix microarrays frmatools altcdfenvs
updated 8.0 years ago by ▴ 830 • written 8.0 years ago by • 0
2
votes
3
replies
2.1k
views
Importing affymetrix genotype calls with GWASTools
gwastools genotype affymetrix microarrays
updated 10.4 years ago by ▴ 890 • written 10.4 years ago by ▴ 40
1
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3
replies
1.7k
views
Two microarrays merging (different experiments) - Error with esets (inSilicoMerging package)
inSilicoMerging microarray affymetrix microarrays
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
2
votes
3
replies
2.6k
views
Why are there so many not annotated probes in the PorGene-1_1-st affymetrix array?
affymetrix microarrays pd.porgene.1.1.st annotation probe to gene id pathway analysis
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 60
2
votes
3
replies
3.1k
views
Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
1
vote
3
replies
3.0k
views
How to convert CEL data to Bed/Bim/Fam/VCF for plink
affymetrix microarrays affymetrix 6.0
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
3
votes
3
replies
3.4k
views
Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays microarray pd.hta.2.0 oligo rma
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
3
votes
3
replies
3.1k
views
Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster.db hugene20sthsentrezg or hugene20stprobeset
affymetrix microarrays hugene20sttranscriptcluster.db
updated 9.6 years ago by 68k • written 9.6 years ago by ▴ 10
0
votes
3
replies
4.8k
views
How do I choose between using affy or oligo package for preprocessing microarrays?
microarray affymetrix microarrays affy oligo
updated 5.0 years ago by 68k • written 9.1 years ago by • 0
2
votes
3
replies
2.1k
views
Problem with memory limit in Rstudio/Windows when importing Affymetrix HTA 2.0 CEL files with oligo R package
oligo hta2.0 affymetrix microarrays memory problem
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 840
0
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2
replies
2.0k
views
Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 9.5 years ago by ★ 4.1k • written 9.5 years ago by ▴ 80
1
vote
2
replies
1.6k
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
2
votes
2
replies
1.8k
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Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
7.3 years ago 2323982403 ▴ 60
1
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2
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4.0k
views
prcomp show "Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded"
prcomp affymetrix microarrays
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
1
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2
replies
2.6k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 10.1 years ago by ▴ 870 • written 10.1 years ago by ▴ 840
0
votes
2
replies
1.8k
views
How to know which Microarray Technique was used to processes the files
R microarray affymetrix microarrays
updated 8.7 years ago by ★ 1.1k • written 8.7 years ago by • 0
2
votes
2
replies
2.2k
views
Problem with GEOquery R package in Windows when trying to download specific GEO processed data
geoquery affymetrix microarrays windows8 getGEO
updated 8.9 years ago by 21k • written 8.9 years ago by ▴ 840
0
votes
2
replies
3.3k
views
How to convert probe sets to Gene symbols ?
affylmgui affymetrix microarrays hgu133plus2
updated 10.2 years ago by ▴ 370 • written 10.2 years ago by • 0
2
votes
2
replies
3.0k
views
Correct creation of design matrix in limma regarding a multi-level experiment
limma multiple factor design affymetrix microarrays limma paired analysis
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 840
0
votes
2
replies
2.0k
views
HuGene20st - lincRNA annotation
hugene20sttranscriptcluster.db lincRNA annotation Affymetrix microarrays HuGene20st
updated 10.7 years ago by 68k • written 10.7 years ago by • 0
1
vote
2
replies
1.4k
views
Determining Mismatch (MM) and perfect match (PM) chip design
affymetrix microarrays
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 10
0
votes
1
reply
1.5k
views
What is the name of this probe?
affymetrix microarrays hta20transcriptcluster r select
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
1
reply
2.1k
views
.DTT file Affymetrix
microarray affymetrix microarrays analysis
updated 10.4 years ago by ★ 4.1k • written 10.4 years ago by • 0
0
votes
1
reply
1.6k
views
Error when trying to read cel affymetrix file with custom platform
affymetrix microarrays ae2bioc getAE
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
0
votes
1
reply
1.7k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
0
votes
1
reply
1.6k
views
nsFilter not filtering out all of the normgene->exon.
genefilter affymetrix microarrays
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
0
votes
1
reply
1.7k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 9.6 years ago by ▴ 420 • written 9.6 years ago by ▴ 840
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Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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