Showing : Oligo • reset
6
votes
22
replies
2.5k
views
Oligo package: paCalls questions
microarray oligo
updated 7.0 years ago by ★ 3.9k • written 7.0 years ago by ▴ 20
0
votes
8
replies
1.0k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 15.3 years ago by ★ 7.4k • written 15.3 years ago by ★ 2.2k
0
votes
7
replies
834
views
presence/absence call using oligo array?
Microarray oligo Microarray oligo
16.4 years ago xpeng ▴ 60
2
votes
14
replies
2.7k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma oligo annotation
updated 7.2 years ago by ▴ 120 • written 7.4 years ago by • 0
0
votes
10
replies
1.2k
views
One-color spotted microarrays analysis
Microarray Normalization oligo Microarray Normalization oligo
updated 13.0 years ago by 13k • written 13.0 years ago by ▴ 30
0
votes
9
replies
912
views
RE: Advice on print-tip normalization
Cancer probe marray oligo Cancer probe marray oligo
updated 17.7 years ago by ▴ 50 • written 17.7 years ago by ▴ 70
3
votes
4
replies
2.3k
views
pd.huex.1.0.st.v2 package doubt
oligo exon array analysis
updated 7.0 years ago by ★ 7.2k • written 7.0 years ago by ▴ 30
0
votes
15
replies
1.8k
views
PreFiltering probe in microarray analysis
Microarray limma oligo Microarray limma oligo
updated 11.0 years ago by ▴ 220 • written 11.0 years ago by ▴ 30
0
votes
6
replies
939
views
Normalization between arrays for common reference, time course and direct two color designs
Normalization limma oligo Normalization limma oligo
15.5 years ago Jenny Drnevich ★ 2.2k
0
votes
5
replies
2.0k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 7.9 years ago by ▴ 160 • written 8.0 years ago by 59k
0
votes
5
replies
870
views
Development of GCRMA-like methods
gcrma oligo gcrma oligo
18.3 years ago Matthew Hannah ▴ 940
0
votes
4
replies
1.2k
views
memory error on unix
oligo oligo
updated 15.0 years ago by ▴ 30 • written 15.0 years ago by ▴ 120
0
votes
3
replies
807
views
makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays
Annotation oligo Annotation oligo
12.9 years ago Jack Schonbrun ▴ 50
0
votes
3
replies
632
views
one-color oligo methods
Normalization oligo Normalization oligo
updated 19.3 years ago by 13k • written 19.3 years ago by ★ 1.4k
3
votes
4
replies
1.4k
views
lm.fit incompatible dimensions
oligo arrayexpress limma
updated 2.3 years ago by • 0 • written 3.4 years ago by • 0
1
vote
5
replies
1.7k
views
Affymetrix Rat Transcriptome Array (Clariom D) annotation
annotation microarray pdinfobuilder oligo
5.7 years ago Ed D • 0
1
vote
8
replies
6.4k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
6.8 years ago Claudia ▴ 10
6
votes
8
replies
1.4k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy aroma.affymetrix exon array xps oligo
4.9 years ago Gordon Smyth 45k
10
votes
13
replies
3.2k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 10
3
votes
9
replies
3.4k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray normalization oligo
updated 6.5 years ago by • 0 • written 7.6 years ago by ▴ 30
3
votes
5
replies
1.1k
views
Farms/Call.INI using oligo package?
probe affy oligo farms probe affy oligo farms
updated 8.5 years ago by ▴ 210 • written 8.5 years ago by ▴ 270
0
votes
4
replies
1.7k
views
Reading Affymetrix data from pd.hugene.2.0.st using oligo/affy
affy oligo
updated 6.2 years ago by ▴ 90 • written 7.3 years ago by ▴ 50
2
votes
16
replies
1.9k
views
Possible ways of performing non-specific intensity filtering on Perfect-match only affymetrix array
oligo DABG non-specific filtering primeview
7.1 years ago svlachavas ▴ 780
0
votes
2
replies
1.5k
views
differences among pd.mogene.1.0.st.v1, mogene10sttranscriptcluster.db and mogene10stprobeset.db
Annotation oligo Annotation oligo
updated 9.7 years ago by 59k • written 9.7 years ago by ▴ 840
0
votes
2
replies
599
views
Nimblegen data analysis
GO cdf affy oligo GO cdf affy oligo
updated 15.0 years ago by ▴ 140 • written 15.0 years ago by ★ 2.2k
0
votes
12
replies
3.1k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
9.3 years ago James W. MacDonald 59k
0
votes
3
replies
1.7k
views
oligo package attaching phenodata for HuGene2.0 ST array
oligo oligo
updated 8.8 years ago by 59k • written 8.8 years ago by ★ 12k
0
votes
4
replies
3.2k
views
An error in oligo: All the CEL files must be of the same type??
BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism
updated 11.0 years ago by ★ 4.3k • written 11.0 years ago by ▴ 20
0
votes
11
replies
2.4k
views
SNP6 data to VCF
SNP oligo ASSIGN SNP oligo ASSIGN
updated 3.7 years ago by • 0 • written 10.3 years ago by 21k
0
votes
8
replies
1.1k
views
crlmm warning
oligo crlmm oligo crlmm
updated 15.2 years ago by ★ 4.3k • written 15.2 years ago by ▴ 190
0
votes
5
replies
768
views
Looking for R package for Nimblegen expression data
oligo makePlatformDesign oligo makePlatformDesign
15.3 years ago Xinxia Peng ▴ 120
0
votes
3
replies
719
views
Fwd: pmStrand() in oligo (version...)
SNP oligo SNP oligo
15.0 years ago Benilton Carvalho ★ 4.3k
3
votes
4
replies
1.2k
views
cause 'memory not mapped' when use oligo
oligo oligoClasses oligo oligoClasses
updated 9.7 years ago by ▴ 50 • written 9.7 years ago by ★ 1.3k
0
votes
17
replies
6.8k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation Normalization GO PROcess oligo Annotation Normalization GO PROcess oligo
updated 9.2 years ago by 59k • written 9.2 years ago by ▴ 100
0
votes
2
replies
1.1k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ▴ 120
0
votes
3
replies
832
views
Spatial Correction
SNP Normalization affy oligo SNP Normalization affy oligo
updated 15.6 years ago by ▴ 120 • written 15.6 years ago by ▴ 170
0
votes
8
replies
1.3k
views
pdInfoBuilder: invalid class object ("ScalarCharacter")
Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder
updated 12.1 years ago by 6.6k • written 12.1 years ago by ★ 3.2k
0
votes
2
replies
1.1k
views
FW: PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 11.5 years ago by ▴ 120 • written 11.5 years ago by ▴ 10
0
votes
3
replies
840
views
oligo package cannot read files when gdata is loaded
Biobase oligo Biobase oligo
12.3 years ago Benilton Carvalho ★ 4.3k
0
votes
2
replies
542
views
spot weight in limma
oligo ASSIGN oligo ASSIGN
17.6 years ago Ren Na ▴ 250
0
votes
3
replies
1.1k
views
[MAANOVA] Warnings in fitmaanova & information request
maanova oligo maanova oligo
12.2 years ago Maciej Jończyk ▴ 720
0
votes
2
replies
991
views
vsn and oligo (or xps?) packages for GeneST expression arrays
vsn oligo xps vsn oligo xps
updated 12.4 years ago by ★ 3.9k • written 12.4 years ago by ▴ 270
0
votes
2
replies
967
views
Affymetrix Gene Chip Normalization
Normalization affy oligo xps Normalization affy oligo xps
updated 10.9 years ago by ★ 3.9k • written 10.9 years ago by ▴ 30
0
votes
4
replies
808
views
Oligo error on OS X Leopard
Cancer oligo Cancer oligo
updated 12.9 years ago by 6.6k • written 12.9 years ago by ★ 1.9k
0
votes
4
replies
615
views
VSN exclusion of probes
probe vsn oligo probe vsn oligo
updated 15.5 years ago by 13k • written 15.5 years ago by ▴ 330
0
votes
2
replies
790
views
Loading Niblegen Files to Oligo
oligo oligo
updated 11.6 years ago by ★ 4.3k • written 11.6 years ago by ▴ 10
0
votes
5
replies
627
views
Inconsistency in RMA results from 'affy' and results from 'oligo'
Annotation cdf oligo Annotation cdf oligo
updated 12.8 years ago by 13k • written 12.8 years ago by ▴ 940
0
votes
2
replies
853
views
Which method best fit nylon single channel technology ?
affy limma oligo affy limma oligo
updated 16.5 years ago by ▴ 10 • written 16.5 years ago by ▴ 160
0
votes
5
replies
731
views
What to do with multiple probes?
Microarray Normalization probe oligo Microarray Normalization probe oligo
updated 16.5 years ago by ★ 5.5k • written 16.5 years ago by ▴ 100
0
votes
4
replies
1.1k
views
Help with Affy TilingArray makePDpackage
affyio oligo affyio oligo
updated 14.3 years ago by ★ 1.2k • written 14.3 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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