Showing : hgug4112a • reset
3
votes
9
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2.2k
views
Annotation problem while quering hgug4112a.db with function select and duplicates for agilent microarray dataset
limma annotation agilent hgug4112a microarray
7.9 years ago Konstantinos Yeles ▴ 80
0
votes
0
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1.0k
views
virtualArray package
Annotation Preprocessing hgu133plus2 hgug4112a
9.3 years ago Guest User ★ 12k
0
votes
0
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8.6k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
9.5 years ago Guest User ★ 12k
0
votes
1
reply
861
views
hgug4845a.db - error in the lookUp function when running genes.rpt.agi
Annotation hgug4112a Annotation hgug4112a
updated 10.2 years ago by 64k • written 10.2 years ago by ▴ 10
0
votes
0
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1.2k
views
Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
10.7 years ago Daniel Emden ▴ 10
0
votes
0
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1.0k
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Mapping genes to their gene sets for GSEA
Microarray Genetics GO hgu95av2 hgug4112a Microarray Genetics GO hgu95av2 hgug4112a
11.5 years ago Yoo, Seungyeul ▴ 110
0
votes
1
reply
757
views
How to create annotation package for not a supported organism
Annotation GO Organism hgug4112a Annotation GO Organism hgug4112a
updated 12.2 years ago by ★ 6.8k • written 12.3 years ago by ▴ 90
0
votes
0
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927
views
FW: normalization one color microarrays
Normalization hgug4112a PROcess Agi4x44PreProcess Normalization hgug4112a PROcess
12.3 years ago Paz Tapia Ramirez ▴ 150
0
votes
1
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1.1k
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 13.4 years ago by ▴ 460 • written 13.4 years ago by ▴ 20
0
votes
1
reply
829
views
Problem with createAnnObjs.HUMANCHIP_DB
hgug4112a RmiR hgug4112a RmiR
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 10
0
votes
2
replies
883
views
Agilent annotation source
Annotation hgug4112a oligo Annotation hgug4112a oligo
updated 13.9 years ago by 64k • written 13.9 years ago by ▴ 990
0
votes
0
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824
views
Questions on the package "RmiR"
miRNA hgug4112a RmiR miRNA hgug4112a RmiR
13.9 years ago jason0701 ▴ 190
0
votes
0
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778
views
Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
hgug4112a probe limma Agi4x44PreProcess hgug4112a probe limma Agi4x44PreProcess
14.0 years ago Pedro Lopez-Romero ▴ 120
0
votes
0
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1.3k
views
on the meaning and value of $stdev.unscaled in a limma's lmFitted MArrayLM object
GO hgug4112a probe GO hgug4112a probe
14.0 years ago Massimo Pinto ▴ 390
0
votes
0
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763
views
error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
Annotation hgug4112a Annotation hgug4112a
14.1 years ago Massimo Pinto ▴ 390
0
votes
3
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1.7k
views
error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
hgug4112a hgug4112a
updated 14.1 years ago by ★ 5.5k • written 14.1 years ago by ▴ 390
0
votes
11
replies
1.7k
views
Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
hgug4112a hgug4112a
updated 14.1 years ago by ★ 1.3k • written 14.1 years ago by ▴ 390
0
votes
2
replies
9.0k
views
an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
GO hgug4112a GO hgug4112a
updated 14.1 years ago by 64k • written 14.1 years ago by ▴ 390
0
votes
0
replies
778
views
build.mappings() from Agi4x44PreProcess is not helping me today
GO GUI hgug4112a limma PROcess Agi4x44PreProcess GO GUI hgug4112a limma PROcess
14.4 years ago Massimo Pinto ▴ 390
0
votes
1
reply
1.1k
views
GOstats: HyperGTest for KEGG
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
updated 14.9 years ago by ★ 7.2k • written 14.9 years ago by ▴ 180
0
votes
0
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1.1k
views
GOstats: hyperGTest for KEGG with org.Sc.sgd.db
Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO
14.9 years ago Paul Evans ▴ 180
0
votes
2
replies
1.6k
views
Agilent G4112F with hgug4112a.db?
GO hgug4112a GO hgug4112a
updated 15.1 years ago by ★ 1.3k • written 15.1 years ago by ▴ 190
0
votes
1
reply
871
views
Agilent spike-in probes
Annotation Normalization GO hgug4112a limma Annotation Normalization GO hgug4112a limma
updated 15.7 years ago by 21k • written 15.7 years ago by ▴ 600
0
votes
1
reply
831
views
Agilent spike-in probes
Annotation Normalization GO hgug4112a limma Annotation Normalization GO hgug4112a limma
updated 15.7 years ago by ★ 6.0k • written 15.7 years ago by 21k
24 results • Page 1 of 1
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Comment: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)? No, you should not apply any batch correction before …
Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
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