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affymetrixchip
•
reset
5
votes
9
replies
3.1k
views
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
replies
1.9k
views
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
replies
3.5k
views
Filtering on present/absent calls methodology and perfect match only arrays
bioconductor
mas5
perfectmatch
affymetrixchip
filter
updated 9.2 years ago by
James W. MacDonald
65k • written 9.2 years ago by
svlachavas
▴ 830
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
2
votes
2
replies
858
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
22 months ago
Yang Shi
▴ 10
2
votes
2
replies
655
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
12 months ago
Abdul
▴ 20
2
votes
2
replies
978
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
3.0 years ago
geoffrey
▴ 10
2
votes
4
replies
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
replies
1.1k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1
oligo
AffymetrixChip
23 months ago • updated 22 months ago
Yang Shi
▴ 10
2
votes
2
replies
556
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
18 months ago
evan.j.williams
▴ 10
2
votes
5
replies
3.0k
views
miRNA expression analysis : annotation
miRNA
annotation
affymetrixchip
9.0 years ago
aswathym
▴ 10
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
1
vote
3
replies
1.5k
views
BioNet package network analysis important questions for tutorial
BioNet
bioconductor
affymetrixchip
network analysis
9.1 years ago
svlachavas
▴ 830
1
vote
1
reply
752
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip
RMA
updated 17 months ago by
Mike Smith
★ 6.5k • written 17 months ago by
Sara
▴ 10
1
vote
4
replies
660
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
11 months ago • updated 8 months ago
richardallenfriedmanbrooklyn
▴ 20
1
vote
2
replies
481
views
Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db
chiptype
chipster
hgu133plus2.db
AffymetrixChip
10 months ago
alexia.brunel
• 0
0
votes
4
replies
373
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
5 weeks ago • updated 4 weeks ago
Efra
• 0
0
votes
0
replies
2.2k
views
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
9.1 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
alakatos
▴ 130 • written 9.0 years ago by
kanacska
▴ 10
0
votes
2
replies
744
views
How to extract probe level intensity after rma() normalization
MicroarrayData
AffymetrixChip
updated 24 months ago by
James W. MacDonald
65k • written 24 months ago by
Haoran
• 0
0
votes
1
reply
864
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
0
votes
1
reply
468
views
Affymetrix hgu133plus2.db: How to best derive an expression value for genes that map to multiple probe ids
affydata
hgu133plus2.db
AffymetrixChip
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
Matthias Munz
▴ 10
0
votes
4
replies
906
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
2.1 years ago
Haoran
• 0
0
votes
0
replies
504
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
Marc Carlson
★ 7.2k • written 13.0 years ago by
Martha Behnke
▴ 100
26 results • Page
1 of 1
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Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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