Showing : Affymetrix microarrays • reset
1
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8
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"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
8.8 years ago Claudia ▴ 10
10
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13
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4.3k
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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 8.8 years ago by • 0 • written 8.8 years ago by ▴ 10
1
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34
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3.8k
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how to check which probesets belong to which transcript?
xps affymetrix microarrays humangene2.0ST micro array data
updated 8.1 years ago by ★ 3.9k • written 8.1 years ago by ▴ 110
0
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3
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3.7k
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How do I choose between using affy or oligo package for preprocessing microarrays?
microarray affymetrix microarrays affy oligo
updated 3.2 years ago by 65k • written 7.3 years ago by • 0
5
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4
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3.2k
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How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
6.3 years ago rahil ▴ 30
2
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10
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3.1k
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matching probes to genes from pd.porgene.1.1.st array
pd.porgene.1.1.st affymetrix microarrays
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 60
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2
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2.9k
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prcomp show "Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded"
prcomp affymetrix microarrays
updated 6.6 years ago by 65k • written 6.6 years ago by • 0
3
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6
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2.6k
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WGCNA normalized CDF to use, WGCNA Intramodular connectivity
wgcna affymetrix microarrays affy
updated 8.8 years ago by ★ 3.0k • written 8.9 years ago by ▴ 30
3
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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 8.1 years ago by 65k • written 8.1 years ago by • 0
0
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0
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2.6k
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Problem with the colors in the heatmap.2 function and the color key values range
gplots heatmap.2 affymetrix microarrays color key
8.7 years ago • updated 8.6 years ago svlachavas ▴ 830
2
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2
replies
2.6k
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Correct creation of design matrix in limma regarding a multi-level experiment
limma multiple factor design affymetrix microarrays limma paired analysis
updated 8.7 years ago by 50k • written 8.7 years ago by ▴ 830
3
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3
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2.2k
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Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster.db hugene20sthsentrezg or hugene20stprobeset
affymetrix microarrays hugene20sttranscriptcluster.db
updated 7.8 years ago by 65k • written 7.8 years ago by ▴ 10
1
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5
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2.2k
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Removing batch effect from microarray data
removebatcheffect() microarray affymetrix microarrays
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 40
1
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6
replies
2.2k
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How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 6.1 years ago by ★ 3.9k • written 6.1 years ago by ▴ 260
0
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2
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2.2k
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How to convert probe sets to Gene symbols ?
affylmgui affymetrix microarrays hgu133plus2
updated 8.4 years ago by ▴ 360 • written 8.4 years ago by • 0
1
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3
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2.1k
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How to convert CEL data to Bed/Bim/Fam/VCF for plink
affymetrix microarrays affymetrix 6.0
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
12
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20
replies
2.0k
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Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 830
2
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3
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2.0k
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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 8.3 years ago by 65k • written 8.3 years ago by ▴ 60
1
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2
replies
1.9k
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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 8.2 years ago by ▴ 850 • written 8.2 years ago by ▴ 830
1
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6
replies
1.9k
views
Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 6.9 years ago by ★ 13k • written 6.9 years ago by • 0
0
votes
0
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1.9k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
8.3 years ago • updated 8.2 years ago svlachavas ▴ 830
2
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4
replies
1.9k
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 8.2 years ago by 25k • written 8.2 years ago by ▴ 830
4
votes
8
replies
1.9k
views
Annotation Problem regarding double platform merged microarray eset using the inSilicoMerging R package, after differential expression analysis
inSilicoMerging doubleannotation affymetrix microarrays limma inSilicoDB
8.7 years ago svlachavas ▴ 830
11
votes
16
replies
1.8k
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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 8.6 years ago by 65k • written 8.6 years ago by ▴ 830
4
votes
7
replies
1.7k
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Understanding the output of the exprs() function
affymetrix microarrays
updated 8.0 years ago by 65k • written 8.0 years ago by • 0
4
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7
replies
1.7k
views
Downloading microarray data for DEG analysis!
affymetrix microarrays
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 10
0
votes
1
reply
1.7k
views
.DTT file Affymetrix
microarray affymetrix microarrays analysis
updated 8.6 years ago by ★ 3.9k • written 8.6 years ago by • 0
1
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1
reply
1.6k
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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 7.7 years ago by ▴ 650 • written 7.7 years ago by ▴ 830
1
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4
replies
1.6k
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How to extract common genes that are DE in each comparisons?
limma bioconductor affymetrix microarrays R
7.3 years ago rkp • 0
2
votes
3
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1.6k
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 7.1 years ago by 65k • written 7.1 years ago by ▴ 830
2
votes
2
replies
1.6k
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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 7.1 years ago by 21k • written 7.1 years ago by ▴ 830
12
votes
6
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1.6k
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Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
2
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3
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1.6k
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Importing affymetrix genotype calls with GWASTools
gwastools genotype affymetrix microarrays
updated 8.6 years ago by ▴ 870 • written 8.6 years ago by ▴ 40
2
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3
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1.5k
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Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
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2
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1.5k
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HuGene20st - lincRNA annotation
hugene20sttranscriptcluster.db lincRNA annotation Affymetrix microarrays HuGene20st
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
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2
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1.4k
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 7.6 years ago by ★ 3.9k • written 7.6 years ago by ▴ 70
0
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1
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1.4k
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Error in Expression File Creator
microarray software error affymetrix microarrays
6.4 years ago parin.kamseng • 0
0
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4
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1.4k
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contrast matrix design for a comparison (trend) of drug concentrations
limma contrast matrix affymetrix microarrays limma
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 840
1
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3
replies
1.4k
views
How to normalize Microarray expression data?
r affymetrix microarrays normalization bioconductor
updated 6.6 years ago by 65k • written 6.6 years ago by ▴ 110
3
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4
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1.4k
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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 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 830
3
votes
4
replies
1.3k
views
Different annotation obtained from hgu133a2.db and affymetrix annotation release
annotation hgu133plus2.db affymetrix microarrays micorarray
updated 5.4 years ago by 65k • written 5.4 years ago by ▴ 60
0
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0
replies
1.3k
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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
7.0 years ago svlachavas ▴ 830
0
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0
replies
1.3k
views
Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
oligo rnadegradationplot affymetrix microarrays pd.hugene.2.0.st
8.2 years ago Biologist ▴ 110
0
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1
reply
1.3k
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Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 830
0
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1
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1.3k
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Error when trying to read cel affymetrix file with custom platform
affymetrix microarrays ae2bioc getAE
updated 8.5 years ago by 65k • written 8.5 years ago by • 0
0
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1
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1.3k
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Getting data from GEO
affymetrix microarrays GEO geoquery
updated 8.4 years ago by 65k • written 8.4 years ago by • 0
0
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0
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1.3k
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Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.6 years ago svlachavas ▴ 830
2
votes
2
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1.2k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
5.5 years ago 2323982403 ▴ 60
0
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1
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1.2k
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nsFilter not filtering out all of the normgene->exon.
genefilter affymetrix microarrays
updated 8.2 years ago by 65k • written 8.2 years ago by • 0
0
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2
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1.2k
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How to know which Microarray Technique was used to processes the files
R microarray affymetrix microarrays
updated 6.8 years ago by ★ 1.0k • written 6.8 years ago by • 0
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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