Showing : Affymetrix • reset
5
votes
9
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4.2k
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Looking for annotation file for Affymetrix SNP 6.0
copynumber snp affymetrix
8.4 years ago KB ▴ 50
2
votes
6
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1.6k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
9.1 years ago svlachavas ▴ 830
3
votes
15
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2.7k
views
Are the p-values supposed to be on the order of 10^-120?
limma affy bioconductor affymetrix
updated 9.5 years ago by 50k • written 9.5 years ago by • 0
6
votes
5
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1.8k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes expression affymetrix pd.hugene.2.0.st limma
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 200
2
votes
4
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2.1k
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Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 9.0 years ago by 65k • written 9.0 years ago by • 0
0
votes
1
reply
1.3k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 4.4 years ago by • 0 • written 5.3 years ago by ★ 3.9k
0
votes
1
reply
2.0k
views
RNA degradation plot: why curves are so smooth?
normalization microarray affymetrix
updated 9.3 years ago by 65k • written 9.3 years ago by • 0
2
votes
2
replies
1.0k
views
Is it possible some statistical evaluation with a few replicates and one control in microarray data analysis in r
r bioconductor affymetrix differential gene expression
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 830
0
votes
2
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1.6k
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Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
data integration microarray bioconductor affymetrix biomarkers
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 830
5
votes
5
replies
1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
3
votes
4
replies
1.4k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by • 0
0
votes
1
reply
1.9k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
1
reply
857
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
0
votes
2
replies
1.7k
views
How to convert .CEL file to .VCF file?
vcf cell affymetrix
2.8 years ago jesus • 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
1
vote
2
replies
801
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
3
votes
1
reply
1.5k
views
what is fitProbeLevelModel()? doing
affymetrix oligo microarray
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 20
0
votes
1
reply
1.8k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray affymetrix oligo RMA normalization
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 20
3
votes
8
replies
2.3k
views
Error aroma.affymetrix [affxparser Fusion SDK exception]
affymetrix affxparser
updated 8.3 years ago by ★ 2.4k • written 8.3 years ago by ▴ 40
0
votes
3
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1.5k
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma affymetrix barcode
updated 8.2 years ago by ▴ 830 • written 8.2 years ago by • 0
1
vote
5
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1.8k
views
Filtering genes with missing Entrez ID using "nsFilter"
nsfilter affymetrix hugene10sttranscriptcluster.db annotation
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
6
votes
7
replies
3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 23 months ago by ▴ 10 • written 7.0 years ago by ▴ 830
0
votes
2
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1.4k
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Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
qc qualitycontrol arrayqualitymetrics mouse gene st 2.0 affymetrix
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
4
votes
5
replies
2.2k
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Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 6.5 years ago by ★ 6.5k • written 6.5 years ago by • 0
0
votes
1
reply
901
views
Affy Mouse Annotation
annotation affymetrix
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
3
votes
3
replies
1.1k
views
Limma: Don't have .CEL Affymatrix Files.
limma affymetrix
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 10
0
votes
1
reply
708
views
differential expression analysis of rice
microarray differential expression analysis GPL2025 affymetrix
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
0
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7
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2.0k
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Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 5.0 years ago by ★ 3.9k • written 5.0 years ago by • 0
0
votes
3
replies
682
views
Input files for Affymetrix platform
Affymetrix CEL TXT
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 50
0
votes
0
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974
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Remove coexpressed gene pair modules using eisa package
isa2 eisa microarray affymetrix
8.9 years ago dhwani.dholakia • 0
0
votes
1
reply
1.2k
views
Filtering out lowly expressed genes on Affymetrix Gene ST arrays
Affymetrix Gene ST limma
8.9 years ago knaxerova ▴ 10
0
votes
0
replies
1.4k
views
News: Rebuilding annotation packages for Affymetrix Gene/Exon ST Arrays
affymetrix annotation microarray News
8.9 years ago James W. MacDonald 65k
0
votes
1
reply
1.3k
views
extract raw expression values in oligo package
oligo affymetrix raw expression
8.7 years ago queso012 • 0
0
votes
0
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2.2k
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MAplot: Binning grid too coarse for current (small) bandwidth
affy affymetrix affymetrics affymetrixchip
9.3 years ago neverstop • 0
0
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0
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1.0k
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QC for Affymetrix Arrays
affymetrix affymetrix microarrays aroma
7.8 years ago gaiusjaugustus • 0
0
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1
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1.2k
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Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
5.7 years ago CantExitVIM ▴ 10
36 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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