Showing : AffymetrixChip • reset
2
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170
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 19 days ago by 67k • written 19 days ago by • 0
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206
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Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles AffymetrixChip
5 months ago drexjaramel • 0
0
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4
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708
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Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
8 months ago Efra • 0
0
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1
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783
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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 16 months ago by ★ 4.6k • written 16 months ago by ▴ 20
1
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2
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748
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Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db chiptype chipster hgu133plus2.db AffymetrixChip
18 months ago alexia.brunel • 0
1
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4
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982
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How to annotate mir4.1 arrays?
AffymetrixChip miRNA oligo
19 months ago • updated 16 months ago richardallenfriedmanbrooklyn ▴ 30
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729
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Volcano plot
limma AffymetrixChip
19 months ago e.gunaut • 0
2
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2
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889
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
20 months ago Abdul ▴ 20
1
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1
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1.0k
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Strange error with RMA during Affymetrix data analysis
AffymetrixChip RMA
updated 2.1 years ago by ★ 6.6k • written 2.1 years ago by ▴ 20
2
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2
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736
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
2.1 years ago evan.j.williams ▴ 10
2
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2
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1.1k
views
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
2.5 years ago Yang Shi ▴ 10
2
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5
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1.3k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1 oligo AffymetrixChip
2.5 years ago Yang Shi ▴ 10
2
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4
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1.4k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219 oligo AffymetrixChip
2.6 years ago Yang Shi ▴ 10
4
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10
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2.3k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
2.6 years ago Yang Shi ▴ 10
0
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2
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977
views
How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
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4
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1.1k
views
getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.7 years ago Haoran • 0
2
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2
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1.2k
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
3.6 years ago geoffrey ▴ 10
0
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1
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1.1k
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.7 years ago by ★ 4.1k • written 3.7 years ago by • 0
3
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2
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1.7k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 9.1 years ago by 67k • written 9.1 years ago by • 0
0
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4
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2.5k
views
HUgene 2.0 analyses heatmap
hugene20 heatmap affymetrixchip
updated 9.6 years ago by ▴ 130 • written 9.6 years ago by ▴ 10
2
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5
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3.2k
views
miRNA expression analysis : annotation
miRNA annotation affymetrixchip
9.6 years ago aswathym ▴ 10
0
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0
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1.3k
views
Correst use of GeneOverlap R Package
GeneOverlap DEGgenes affymetrixchip bioconductor
9.7 years ago svlachavas ▴ 840
1
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3
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1.7k
views
BioNet package network analysis important questions for tutorial
BioNet bioconductor affymetrixchip network analysis
9.7 years ago svlachavas ▴ 840
5
votes
9
replies
3.5k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
9.8 years ago • updated 9.7 years ago svlachavas ▴ 840
1
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4
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3.7k
views
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis
9.8 years ago svlachavas ▴ 840
3
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11
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3.8k
views
Filtering on present/absent calls methodology and perfect match only arrays
bioconductor mas5 perfectmatch affymetrixchip filter
updated 9.8 years ago by 67k • written 9.8 years ago by ▴ 840
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0
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2.4k
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MAplot: Binning grid too coarse for current (small) bandwidth
affy affymetrix affymetrics affymetrixchip
9.9 years ago neverstop • 0
0
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1
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2.0k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 13.6 years ago by ★ 7.2k • written 13.6 years ago by ▴ 100
28 results • Page 1 of 1
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Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output by ATpoint ★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
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Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
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