Showing : affymetrixchip • reset
5
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9
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3.1k
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Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
9.1 years ago svlachavas ▴ 830
4
votes
10
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1.9k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
3
votes
11
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3.5k
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Filtering on present/absent calls methodology and perfect match only arrays
bioconductor mas5 perfectmatch affymetrixchip filter
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 830
3
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2
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1.5k
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Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 8.4 years ago by 65k • written 8.4 years ago by • 0
2
votes
2
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849
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How to compute P/A calls at gene-level probeset of Human Gene 1.0 ST Array
pd.hugene.1.0.st.v1 oligo AffymetrixChip
22 months ago Yang Shi ▴ 10
2
votes
2
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638
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
12 months ago Abdul ▴ 20
2
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2
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968
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Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
2.9 years ago geoffrey ▴ 10
2
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4
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1.1k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219 oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
2
votes
5
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1.0k
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Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1 oligo AffymetrixChip
22 months ago Yang Shi ▴ 10
2
votes
2
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543
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
18 months ago evan.j.williams ▴ 10
2
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5
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2.9k
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miRNA expression analysis : annotation
miRNA annotation affymetrixchip
9.0 years ago aswathym ▴ 10
1
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4
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3.4k
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GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis
9.1 years ago svlachavas ▴ 830
1
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3
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1.5k
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BioNet package network analysis important questions for tutorial
BioNet bioconductor affymetrixchip network analysis
9.1 years ago svlachavas ▴ 830
1
vote
1
reply
740
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip RMA
updated 17 months ago by ★ 6.5k • written 17 months ago by ▴ 10
1
vote
4
replies
643
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How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
11 months ago • updated 8 months ago richardallenfriedmanbrooklyn ▴ 20
1
vote
2
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470
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Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db chiptype chipster hgu133plus2.db AffymetrixChip
10 months ago alexia.brunel • 0
0
votes
4
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357
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
4 weeks ago • updated 22 days ago Efra • 0
0
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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
votes
0
replies
1.2k
views
Correst use of GeneOverlap R Package
GeneOverlap DEGgenes affymetrixchip bioconductor
9.0 years ago svlachavas ▴ 830
0
votes
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20 heatmap affymetrixchip
updated 8.9 years ago by ▴ 130 • written 8.9 years ago by ▴ 10
0
votes
2
replies
735
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 23 months ago by 65k • written 23 months 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
1
reply
460
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Affymetrix hgu133plus2.db: How to best derive an expression value for genes that map to multiple probe ids
affydata hgu133plus2.db AffymetrixChip
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
0
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4
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894
views
getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.1 years ago Haoran • 0
0
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0
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498
views
Volcano plot
limma AffymetrixChip
11 months ago e.gunaut • 0
0
votes
1
reply
1.9k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 13.0 years ago by ★ 7.2k • written 13.0 years ago by ▴ 100
26 results • Page 1 of 1
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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 doctor know about Alzheimer and they don't expect significan…
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.
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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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