Showing : hgug4112a • reset
3
votes
9
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3.0k
views
Annotation problem while quering hgug4112a.db with function select and duplicates for agilent microarray dataset
limma annotation agilent hgug4112a microarray
9.6 years ago Konstantinos Yeles ▴ 90
0
votes
0
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1.4k
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virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
11.0 years ago Guest User ★ 13k
0
votes
0
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9.7k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
11.2 years ago Guest User ★ 13k
0
votes
1
reply
1.1k
views
hgug4845a.db - error in the lookUp function when running genes.rpt.agi
Annotation hgug4112a Annotation hgug4112a
updated 11.9 years ago by 68k • written 11.9 years ago by ▴ 10
0
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0
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1.5k
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Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
12.4 years ago Daniel Emden ▴ 10
0
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0
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1.3k
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Mapping genes to their gene sets for GSEA
Microarray Genetics GO hgu95av2 hgug4112a Microarray Genetics GO hgu95av2 hgug4112a
13.3 years ago Yoo, Seungyeul ▴ 110
0
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1
reply
998
views
How to create annotation package for not a supported organism
Annotation GO Organism hgug4112a Annotation GO Organism hgug4112a
updated 14.0 years ago by ★ 6.8k • written 14.0 years ago by ▴ 90
0
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0
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1.2k
views
FW: normalization one color microarrays
Normalization hgug4112a PROcess Agi4x44PreProcess Normalization hgug4112a PROcess
14.0 years ago Paz Tapia Ramirez ▴ 150
0
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1
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1.4k
views
Agi4x44PreProcess: INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = …
hgug4112a Agi4x44PreProcess hgug4112a Agi4x44PreProcess
updated 15.1 years ago by ▴ 460 • written 15.1 years ago by ▴ 20
0
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1
reply
1.0k
views
Problem with createAnnObjs.HUMANCHIP_DB
hgug4112a RmiR hgug4112a RmiR
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 10
0
votes
2
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1.2k
views
Agilent annotation source
Annotation hgug4112a oligo Annotation hgug4112a oligo
updated 15.6 years ago by 68k • written 15.6 years ago by ★ 1.1k
0
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0
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Questions on the package "RmiR"
miRNA hgug4112a RmiR miRNA hgug4112a RmiR
15.6 years ago jason0701 ▴ 190
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0
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1.0k
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Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
hgug4112a probe limma Agi4x44PreProcess hgug4112a probe limma Agi4x44PreProcess
15.7 years ago Pedro Lopez-Romero ▴ 120
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0
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1.5k
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on the meaning and value of $stdev.unscaled in a limma's lmFitted MArrayLM object
GO hgug4112a probe GO hgug4112a probe
15.8 years ago Massimo Pinto ▴ 390
0
votes
0
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1.0k
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error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
Annotation hgug4112a Annotation hgug4112a
15.9 years ago Massimo Pinto ▴ 390
0
votes
3
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2.1k
views
error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
hgug4112a hgug4112a
updated 15.9 years ago by ★ 5.5k • written 15.9 years ago by ▴ 390
0
votes
11
replies
2.5k
views
Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
hgug4112a hgug4112a
updated 15.9 years ago by ★ 1.3k • written 15.9 years ago by ▴ 390
0
votes
2
replies
9.7k
views
an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
GO hgug4112a GO hgug4112a
updated 15.9 years ago by 68k • written 15.9 years ago by ▴ 390
0
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0
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1.1k
views
build.mappings() from Agi4x44PreProcess is not helping me today
GO GUI hgug4112a limma PROcess Agi4x44PreProcess GO GUI hgug4112a limma PROcess
16.2 years ago Massimo Pinto ▴ 390
0
votes
1
reply
1.5k
views
GOstats: HyperGTest for KEGG
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
updated 16.6 years ago by ★ 7.2k • written 16.6 years ago by ▴ 180
0
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0
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1.5k
views
GOstats: hyperGTest for KEGG with org.Sc.sgd.db
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
16.7 years ago Paul Evans ▴ 180
0
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2
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2.0k
views
Agilent G4112F with hgug4112a.db?
GO hgug4112a GO hgug4112a
updated 16.8 years ago by ★ 1.3k • written 16.8 years ago by ▴ 190
0
votes
1
reply
1.1k
views
Agilent spike-in probes
Annotation Normalization GO hgug4112a limma Annotation Normalization GO hgug4112a limma
updated 17.4 years ago by 21k • written 17.4 years ago by ▴ 600
0
votes
1
reply
1.1k
views
Agilent spike-in probes
Annotation Normalization GO hgug4112a limma Annotation Normalization GO hgug4112a limma
updated 17.5 years ago by ★ 6.0k • written 17.5 years ago by 21k
24 results • Page 1 of 1
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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
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