Showing : affymetrix microarrays • reset
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What is the name of this probe?
affymetrix microarrays hta20transcriptcluster r select
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
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3
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1.4k
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Two microarrays merging (different experiments) - Error with esets (inSilicoMerging package)
inSilicoMerging microarray affymetrix microarrays
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
3
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4
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1.6k
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Different annotation obtained from hgu133a2.db and affymetrix annotation release
annotation hgu133plus2.db affymetrix microarrays micorarray
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 60
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2
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1.5k
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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
6.3 years ago 2323982403 ▴ 60
2
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3
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Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
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3
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How to convert CEL data to Bed/Bim/Fam/VCF for plink
affymetrix microarrays affymetrix 6.0
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
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2
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1.2k
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What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
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2
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Determining Mismatch (MM) and perfect match (PM) chip design
affymetrix microarrays
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
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1
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1.1k
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Microarray data analysis
microarry affymetrix microarrays phenotype extraction
updated 6.7 years ago by ★ 1.1k • written 6.7 years ago by • 0
1
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6
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2.6k
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How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 7.0 years ago by ★ 4.1k • written 7.0 years ago by ▴ 260
2
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3
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1.5k
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How to create vectors (makeVectorsAffyBatch) , using own cdf
affymetrix microarrays frmatools altcdfenvs
updated 7.0 years ago by ▴ 830 • written 7.0 years ago by • 0
5
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4
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How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
7.2 years ago rahil ▴ 30
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1.0k
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What package should I use to retrieve chromosome location for Affymetrix id of gene symbol id while doing gene expression microarray analysis ?
affymetrix microarrays differential gene expression
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 20
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1.6k
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Error in Expression File Creator
microarray software error affymetrix microarrays
7.2 years ago parin.kamseng • 0
1
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1
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1.6k
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Trying to annotate microarray data and some probe set presents mismatch
annotation affymetrix microarrays
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
4
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7
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2.2k
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Downloading microarray data for DEG analysis!
affymetrix microarrays
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 10
1
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3
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1.6k
views
How to normalize Microarray expression data?
r affymetrix microarrays normalization bioconductor
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 120
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2
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3.5k
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prcomp show "Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded"
prcomp affymetrix microarrays
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
4
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3
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1.4k
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How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
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3
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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 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
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2
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How to know which Microarray Technique was used to processes the files
R microarray affymetrix microarrays
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by • 0
1
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6
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2.2k
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Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 7.8 years ago by ★ 13k • written 7.8 years ago by • 0
12
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6
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1.8k
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Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
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0
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1.5k
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Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.8 years ago svlachavas ▴ 840
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2
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1.9k
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Problem with GEOquery R package in Windows when trying to download specific GEO processed data
geoquery affymetrix microarrays windows8 getGEO
updated 7.9 years ago by 21k • written 7.9 years ago by ▴ 840
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3
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1.8k
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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 7.9 years ago by 68k • written 7.9 years ago by ▴ 840
1
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5
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2.6k
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Removing batch effect from microarray data
removebatcheffect() microarray affymetrix microarrays
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
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3
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How do I choose between using affy or oligo package for preprocessing microarrays?
microarray affymetrix microarrays affy oligo
updated 4.0 years ago by 68k • written 8.1 years ago by • 0
1
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4
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1.8k
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How to extract common genes that are DE in each comparisons?
limma bioconductor affymetrix microarrays R
8.1 years ago rkp • 0
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4
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1.7k
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contrast matrix design for a comparison (trend) of drug concentrations
limma contrast matrix affymetrix microarrays limma
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 840
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2
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1.7k
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 8.5 years ago by ★ 4.1k • written 8.5 years ago by ▴ 80
1
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1
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1.9k
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Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays sva combat sva batch effect plotMDS
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by ▴ 840
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3
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2.7k
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Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster.db hugene20sthsentrezg or hugene20stprobeset
affymetrix microarrays hugene20sttranscriptcluster.db
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 10
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1.5k
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Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 8.6 years ago by ▴ 420 • written 8.7 years ago by ▴ 840
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1.2k
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QC for Affymetrix Arrays
affymetrix affymetrix microarrays aroma
8.7 years ago gaiusjaugustus • 0
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1.2k
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Job: Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
microarray limma affymetrix microarrays r microarray affy rna-seq Job
8.7 years ago Thomas.F.Hahn2 • 0
4
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7
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2.3k
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Understanding the output of the exprs() function
affymetrix microarrays
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
1
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34
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4.9k
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how to check which probesets belong to which transcript?
xps affymetrix microarrays humangene2.0ST micro array data
updated 8.9 years ago by ★ 3.9k • written 8.9 years ago by ▴ 120
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3
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Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays microarray pd.hta.2.0 oligo rma
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
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0
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In the frmaTools package, how can I makeVectorsFeatureSet() output include probeVecCore like the pre-built vectors?
frma frmatools affymetrix microarrays
9.0 years ago jperezrogers • 0
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859
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Mouse ST 2.1 noncoding
microarray affymetrix microarrays
9.0 years ago miquel.garcia • 0
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1.5k
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Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
oligo rnadegradationplot affymetrix microarrays pd.hugene.2.0.st
9.0 years ago Biologist ▴ 120
0
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1
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1.4k
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nsFilter not filtering out all of the normgene->exon.
genefilter affymetrix microarrays
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
2
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4
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2.1k
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Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
expressionset limma annotation affymetrix microarrays
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 840
1
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2
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2.2k
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 9.1 years ago by ▴ 870 • written 9.1 years ago by ▴ 840
0
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0
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2.1k
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Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
9.1 years ago svlachavas ▴ 840
2
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3
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2.2k
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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 9.1 years ago by 68k • written 9.1 years ago by ▴ 60
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10
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3.5k
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matching probes to genes from pd.porgene.1.1.st array
pd.porgene.1.1.st affymetrix microarrays
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 60
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2
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2.6k
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How to convert probe sets to Gene symbols ?
affylmgui affymetrix microarrays hgu133plus2
updated 9.2 years ago by ▴ 370 • written 9.2 years ago by • 0
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1.5k
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Getting data from GEO
affymetrix microarrays GEO geoquery
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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