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affymetrixchip
•
reset
0
votes
4
replies
298
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 2 days ago
Efra
• 0
1
vote
4
replies
617
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
10 months ago • updated 7 months ago
richardallenfriedmanbrooklyn
▴ 20
0
votes
1
reply
435
views
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
ATpoint
★ 4.0k • written 8 months ago by
Matthias Munz
▴ 10
1
vote
2
replies
446
views
Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db
chiptype
chipster
hgu133plus2.db
AffymetrixChip
9 months ago
alexia.brunel
• 0
0
votes
0
replies
471
views
Volcano plot
limma
AffymetrixChip
11 months ago
e.gunaut
• 0
2
votes
2
replies
611
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
11 months ago
Abdul
▴ 20
1
vote
1
reply
718
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip
RMA
updated 16 months ago by
Mike Smith
★ 6.5k • written 16 months ago by
Sara
▴ 10
2
votes
2
replies
515
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
17 months ago
evan.j.williams
▴ 10
2
votes
2
replies
828
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
21 months ago
Yang Shi
▴ 10
2
votes
5
replies
1.0k
views
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
4
replies
1.1k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219
oligo
AffymetrixChip
22 months ago
Yang Shi
▴ 10
4
votes
10
replies
1.8k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
22 months ago
Yang Shi
▴ 10
0
votes
2
replies
716
views
How to extract probe level intensity after rma() normalization
MicroarrayData
AffymetrixChip
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
Haoran
• 0
0
votes
4
replies
870
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
2.0 years ago • updated 24 months ago
Haoran
• 0
2
votes
2
replies
950
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
2.9 years ago
geoffrey
▴ 10
0
votes
1
reply
839
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
Pierre-Alex
• 0
3
votes
2
replies
1.5k
views
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
James W. MacDonald
65k • written 8.4 years ago by
koreebay
• 0
0
votes
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 8.9 years ago by
alakatos
▴ 130 • written 8.9 years ago by
kanacska
▴ 10
2
votes
5
replies
2.9k
views
miRNA expression analysis : annotation
miRNA
annotation
affymetrixchip
9.0 years ago • updated 8.9 years ago
aswathym
▴ 10
0
votes
0
replies
1.2k
views
Correst use of GeneOverlap R Package
GeneOverlap
DEGgenes
affymetrixchip
bioconductor
9.0 years ago
svlachavas
▴ 830
1
vote
3
replies
1.5k
views
BioNet package network analysis important questions for tutorial
BioNet
bioconductor
affymetrixchip
network analysis
9.0 years ago
svlachavas
▴ 830
5
votes
9
replies
3.0k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor
expresiondataset
affymetrixchip
differential gene expression
9.1 years ago • updated 9.0 years ago
svlachavas
▴ 830
1
vote
4
replies
3.4k
views
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
3
votes
11
replies
3.4k
views
Filtering on present/absent calls methodology and perfect match only arrays
bioconductor
mas5
perfectmatch
affymetrixchip
filter
updated 9.1 years ago by
James W. MacDonald
65k • written 9.1 years ago by
svlachavas
▴ 830
0
votes
0
replies
2.2k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy
affymetrix
affymetrics
affymetrixchip
9.2 years ago
neverstop
• 0
0
votes
1
reply
1.9k
views
Having trouble with new brainarray CDF
Microarray
Annotation
AnnotationData
AffymetrixChip
hgu133a2
cdf
probe
graph
AnnotationDbi
updated 12.9 years ago by
Marc Carlson
★ 7.2k • written 12.9 years ago by
Martha Behnke
▴ 100
26 results • Page
1 of 1
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Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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James W. MacDonald
65k
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Pierre Lindenbaum
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Gordon Smyth
50k
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Jenny Drnevich
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