Showing : affymetrix microarrays • reset
0
votes
3
replies
3.7k
views
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
0
votes
1
reply
1.0k
views
What is the name of this probe?
affymetrix microarrays hta20transcriptcluster r select
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
1
vote
3
replies
1.1k
views
Two microarrays merging (different experiments) - Error with esets (inSilicoMerging package)
inSilicoMerging microarray affymetrix microarrays
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
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
2
votes
2
replies
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
2
votes
3
replies
1.5k
views
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
1
vote
3
replies
2.1k
views
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
1
vote
2
replies
962
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
vote
2
replies
873
views
Determining Mismatch (MM) and perfect match (PM) chip design
affymetrix microarrays
updated 5.8 years ago by 65k • written 5.8 years ago by ▴ 10
1
vote
1
reply
870
views
Microarray data analysis
microarry affymetrix microarrays phenotype extraction
updated 5.8 years ago by ★ 1.0k • written 5.8 years ago by • 0
1
vote
6
replies
2.2k
views
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
2
votes
3
replies
1.2k
views
How to create vectors (makeVectorsAffyBatch) , using own cdf
affymetrix microarrays frmatools altcdfenvs
updated 6.2 years ago by ▴ 830 • written 6.2 years ago by • 0
5
votes
4
replies
3.2k
views
How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
6.3 years ago rahil ▴ 30
0
votes
1
reply
809
views
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 6.4 years ago by 65k • written 6.4 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Error in Expression File Creator
microarray software error affymetrix microarrays
6.4 years ago parin.kamseng • 0
1
vote
1
reply
1.1k
views
Trying to annotate microarray data and some probe set presents mismatch
annotation affymetrix microarrays
updated 6.4 years ago by 65k • written 6.4 years ago by • 0
4
votes
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
1
vote
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
1
vote
2
replies
2.9k
views
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
4
votes
3
replies
1.2k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
1
vote
3
replies
1.1k
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 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
votes
2
replies
1.2k
views
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
1
vote
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
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
0
votes
0
replies
1.3k
views
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
2
votes
2
replies
1.6k
views
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
2
votes
3
replies
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
1
vote
5
replies
2.2k
views
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
vote
4
replies
1.6k
views
How to extract common genes that are DE in each comparisons?
limma bioconductor affymetrix microarrays R
7.3 years ago rkp • 0
0
votes
4
replies
1.4k
views
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
0
votes
2
replies
1.4k
views
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
1
vote
1
reply
1.6k
views
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
3
votes
3
replies
2.2k
views
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
0
votes
1
reply
1.3k
views
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
votes
0
replies
1.1k
views
QC for Affymetrix Arrays
affymetrix affymetrix microarrays aroma
7.9 years ago gaiusjaugustus • 0
0
votes
0
replies
1.1k
views
Job: Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
microarray limma affymetrix microarrays r microarray affy rna-seq Job
7.9 years ago Thomas.F.Hahn2 • 0
4
votes
7
replies
1.7k
views
Understanding the output of the exprs() function
affymetrix microarrays
updated 8.0 years ago by 65k • written 8.0 years ago by • 0
1
vote
34
replies
3.8k
views
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
3
votes
3
replies
2.6k
views
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
votes
0
replies
1.1k
views
In the frmaTools package, how can I makeVectorsFeatureSet() output include probeVecCore like the pre-built vectors?
frma frmatools affymetrix microarrays
8.1 years ago jperezrogers • 0
0
votes
0
replies
744
views
Mouse ST 2.1 noncoding
microarray affymetrix microarrays
8.2 years ago miquel.garcia • 0
0
votes
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
votes
1
reply
1.2k
views
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
2
votes
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
1
vote
2
replies
1.9k
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 8.2 years ago by ▴ 850 • written 8.2 years ago by ▴ 830
0
votes
0
replies
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
votes
3
replies
2.0k
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 8.3 years ago by 65k • written 8.3 years ago by ▴ 60
2
votes
10
replies
3.1k
views
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
0
votes
2
replies
2.2k
views
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
0
votes
1
reply
1.3k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 8.4 years ago by 65k • written 8.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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…
Votes
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
Awards • All
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Locations • All
United Kingdom, 5 minutes ago
Belgium, 5 minutes ago
Germany, 8 minutes ago
EMBL Heidelberg, 9 minutes ago
Austria, 9 minutes ago
Traffic: 696 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6