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pdInfoBuilder
•
reset
2
votes
8
replies
1.2k
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses
oligo
pdInfoBuilder
2.8 years ago
efoss
▴ 10
2
votes
3
replies
1.2k
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray
pdInfoBuilder
oligo
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
Marton Papp
• 0
6
votes
4
replies
2.6k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray
mirna
oligo package
pdinfobuilder
pd.mirna
updated 4.5 years ago by
soumyab.g
▴ 10 • written 6.9 years ago by
rolan.zauner
▴ 20
0
votes
7
replies
1.7k
views
oligo and GenericPDInfo
affy
oligoclasses
oligo package
pdinfobuilder
annotationdbi
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
Aedin Culhane
▴ 510
1
vote
3
replies
3.0k
views
How to analyse clariom d human files
limma
pdinfobuilder
affy
cdf
7.1 years ago
yusuf.khan
▴ 10
3
votes
7
replies
1.7k
views
Oligo: cannot fit robust Probe Level linear Models / fitPLM when using a custom CDF
oligo
pdinfobuilder
pd.mogene.1.1.st
customcdf
updated 7.6 years ago by
James W. MacDonald
65k • written 8.1 years ago by
Guido Hooiveld
★ 3.9k
1
vote
5
replies
2.4k
views
Affymetrix Rat Transcriptome Array (Clariom D) annotation
annotation
microarray
pdinfobuilder
oligo
7.7 years ago • updated 7.6 years ago
Ed D
• 0
0
votes
3
replies
2.7k
views
Draft support for HTA 2.0 with oligo
Annotation
pdInfoBuilder
Annotation
pdInfoBuilder
updated 7.8 years ago by
aswathym
▴ 10 • written 10.2 years ago by
Johann Pellet
▴ 10
1
vote
0
replies
2.3k
views
The current annotation for Affymetrix HTA 2.0 array is problematic
oligo
pdInfoBuilder
pd.hta.2.0
8.8 years ago
tangboyun
▴ 30
0
votes
2
replies
1.3k
views
Error with annotation package with pdInfoBuilder for NimbleGen arrays
pdinfobuilder
oligo
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
george.kararigas
• 0
0
votes
5
replies
1.7k
views
Annotation package built with pdInfoBuilder cannot be installed
annotation
pdinfobuilder
9.1 years ago
alakatos
▴ 130
1
vote
3
replies
2.4k
views
Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
BiocViews
Annotation
Organism
biocViews
pdInfoBuilder
BiocViews
BiocViews
Annotation
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Guilherme Rocha
▴ 40
0
votes
1
reply
1.3k
views
pd.mirna.4.1
pdInfoBuilder
pdInfoBuilder
updated 10.0 years ago by
James W. MacDonald
65k • written 10.0 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
Draft support for HTA 2.0 with oligo
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
10.0 years ago
Elena Serrano
▴ 30
0
votes
0
replies
2.1k
views
Affymetrix HTA 2 array analysis
BiocViews
Annotation
Cancer
Breast
Organism
PROcess
biocViews
pdInfoBuilder
BiocViews
10.0 years ago
Elena Serrano
▴ 30
0
votes
4
replies
6.4k
views
Problem "Error: is.character(filenames) is not TRUE" in read.xysfiles (Oligo package)
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 10.1 years ago by
James W. MacDonald
65k • written 10.1 years ago by
Tommaso Raffaello
▴ 60
0
votes
3
replies
1.2k
views
pdInfoBuilder - problem installing the annotation package
Annotation
pdInfoBuilder
Annotation
pdInfoBuilder
updated 10.1 years ago by
Benilton Carvalho
★ 4.3k • written 10.1 years ago by
Tommaso Raffaello
▴ 60
0
votes
1
reply
1.7k
views
Draft support for HTA 2.0 with oligo
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 10.2 years ago by
Mark Cowley
▴ 910 • written 10.2 years ago by
Benilton Carvalho
★ 4.3k
0
votes
0
replies
3.4k
views
Affymetrix HTA 2 array analysis
BiocViews
Annotation
Cancer
Breast
Organism
PROcess
biocViews
pdInfoBuilder
BiocViews
10.3 years ago
Elena Serrano
▴ 30
0
votes
1
reply
2.0k
views
Affymetrix HTA 2 array analysis
BiocViews
Annotation
Cancer
Breast
Organism
PROcess
biocViews
pdInfoBuilder
BiocViews
updated 10.5 years ago by
Benilton Carvalho
★ 4.3k • written 10.5 years ago by
Stephen Turner
▴ 290
0
votes
1
reply
1.3k
views
upload multiple genelists at a time for GO or pathway enrichment
GO
cdf
oligo
pdInfoBuilder
xps
GO
cdf
oligo
pdInfoBuilder
xps
updated 10.5 years ago by
Pekka Kohonen
▴ 190 • written 10.5 years ago by
Helen Smith
▴ 100
0
votes
1
reply
1.1k
views
Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation
PROcess
pdInfoBuilder
charm
Annotation
PROcess
pdInfoBuilder
charm
updated 10.7 years ago by
Nitesh Turaga
▴ 50 • written 10.7 years ago by
Benilton Carvalho
★ 4.3k
0
votes
1
reply
1.2k
views
Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation
PROcess
pdInfoBuilder
charm
Annotation
PROcess
pdInfoBuilder
charm
10.7 years ago
Nitesh Turaga
▴ 50
0
votes
1
reply
1.4k
views
Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation
PROcess
pdInfoBuilder
charm
Annotation
PROcess
pdInfoBuilder
charm
updated 10.7 years ago by
Benilton Carvalho
★ 4.3k • written 10.7 years ago by
Nitesh Turaga
▴ 50
0
votes
4
replies
1.6k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray
Annotation
GO
Organism
probe
annotate
limma
convert
pdInfoBuilder
sva
GO
sva
updated 10.9 years ago by
Benilton Carvalho
★ 4.3k • written 10.9 years ago by
Johnson, Franklin Theodore
▴ 140
0
votes
10
replies
3.0k
views
PAIR files -- feature set table
Microarray
Annotation
Organism
annotate
pdInfoBuilder
Microarray
Annotation
Organism
updated 10.9 years ago by
Benilton Carvalho
★ 4.3k • written 10.9 years ago by
Guest User
★ 13k
0
votes
7
replies
1.6k
views
install pdInfoBuilder package
Annotation
pdInfoBuilder
Annotation
pdInfoBuilder
updated 11.4 years ago by
Benilton Carvalho
★ 4.3k • written 11.4 years ago by
Julie Collet
▴ 40
0
votes
0
replies
840
views
Nimblegen microarray MM8_60mer_expr
Microarray
Annotation
oligo
pdInfoBuilder
Microarray
Annotation
oligo
pdInfoBuilder
11.5 years ago
Benilton Carvalho
★ 4.3k
0
votes
4
replies
1.5k
views
Passing multiple files to pdInfobuilder
BiocViews
biocViews
pdInfoBuilder
BiocViews
BiocViews
biocViews
pdInfoBuilder
updated 11.5 years ago by
Benilton Carvalho
▴ 50 • written 11.5 years ago by
Guest User
★ 13k
0
votes
3
replies
2.0k
views
oligo and pd.aragene.1.1.st annotation
Annotation
limma
Category
pdInfoBuilder
Annotation
limma
Category
pdInfoBuilder
updated 11.8 years ago by
Marc Carlson
★ 7.2k • written 11.8 years ago by
Stephen Rolfe
▴ 20
0
votes
2
replies
1.2k
views
oligo and pdInfoBuilder
Annotation
Yeast
oligo
pdInfoBuilder
Annotation
Yeast
oligo
pdInfoBuilder
updated 11.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.9 years ago by
Simon Melov
▴ 340
0
votes
0
replies
1.3k
views
Nimblegen promoter medip array platform design file problem
BiocViews
Annotation
Organism
biocViews
pdInfoBuilder
charm
BiocViews
BiocViews
Annotation
12.0 years ago
zeynep özkeserli
▴ 160
0
votes
0
replies
1.3k
views
Nimblegen promoter medip array platform design file problem
BiocViews
Annotation
Organism
biocViews
pdInfoBuilder
charm
BiocViews
BiocViews
Annotation
12.0 years ago
zeynep özkeserli
▴ 160
0
votes
2
replies
1.3k
views
oligo package: extracting position, sequence, and intensity from Affymetrix tiling array
BiocViews
Organism
biocViews
oligo
pdInfoBuilder
BiocViews
BiocViews
Organism
biocViews
updated 12.1 years ago by
Benilton Carvalho
★ 4.3k • written 12.1 years ago by
Guest User
★ 13k
0
votes
2
replies
1.4k
views
pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays
Annotation
oligo
pdInfoBuilder
oligoClasses
Annotation
oligo
pdInfoBuilder
oligoClasses
updated 12.2 years ago by
Benilton Carvalho
★ 4.3k • written 12.2 years ago by
Groot, Philip de
▴ 630
0
votes
0
replies
1.4k
views
Using pdInfoBuilder for Human Exon Array
BiocViews
Annotation
Organism
cdf
biocViews
oligo
pdInfoBuilder
BiocViews
BiocViews
cdf
12.9 years ago
Maria Rodrigo-Domingo / Region Nordjyll…
▴ 10
0
votes
1
reply
973
views
pdInfoBuilder
Annotation
pdInfoBuilder
Annotation
pdInfoBuilder
updated 13.0 years ago by
Benilton Carvalho
★ 4.3k • written 13.0 years ago by
Barbara Bo-Ju Shih
▴ 40
0
votes
3
replies
1.2k
views
Error using pdInfoBuilder for NimbleGen Array
Annotation
pdInfoBuilder
Annotation
pdInfoBuilder
updated 13.2 years ago by
Vincent J. Carey, Jr.
6.7k • written 13.2 years ago by
Kate Turner
▴ 20
0
votes
0
replies
1.1k
views
Need help with pdInfoBuilder package for human ST arrays
Annotation
affy
oligo
pdInfoBuilder
Annotation
affy
oligo
pdInfoBuilder
13.9 years ago
He, Yiwen NIH/CIT
▴ 360
0
votes
2
replies
1.0k
views
pdInfoBuilder -- MOUSEDIVm520650
Annotation
pdInfoBuilder
crlmm
Annotation
pdInfoBuilder
crlmm
updated 14.0 years ago by
James W. MacDonald
65k • written 14.0 years ago by
Ivanek, Robert
▴ 100
0
votes
3
replies
1.2k
views
pdInfoBuider: how to view SQL scheme?
pdInfoBuilder
pdInfoBuilder
updated 14.0 years ago by
Benilton Carvalho
★ 4.3k • written 14.0 years ago by
Guido Hooiveld
★ 3.9k
0
votes
8
replies
2.0k
views
pdInfoBuilder: invalid class object ("ScalarCharacter")
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 14.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.1 years ago by
Guido Hooiveld
★ 3.9k
0
votes
6
replies
1.6k
views
PdInfoBuilder for nimblegen array
Annotation
Organism
oligo
pdInfoBuilder
Annotation
Organism
oligo
pdInfoBuilder
updated 14.2 years ago by
Benilton Carvalho
★ 4.3k • written 14.2 years ago by
Alex Rodriguez
▴ 40
0
votes
0
replies
807
views
TilingFeatureSet
GO
pdInfoBuilder
GO
pdInfoBuilder
14.4 years ago
Diego Martinez
▴ 10
0
votes
1
reply
1.2k
views
Help with Oligo Package: Extracting and Graphing
Transcription
Normalization
Yeast
probe
affy
graph
tilingArray
oligo
pdInfoBuilder
Starr
updated 14.5 years ago by
Tobias Straub
▴ 430 • written 14.5 years ago by
Noah Dowell
▴ 410
0
votes
2
replies
1.7k
views
Affymetrix Mouse Promoter array / pdInfoBuilder
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 14.6 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 14.6 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
0
replies
1.0k
views
problem with pdInfoBuilder
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
15.0 years ago
Elsa Aguera
▴ 10
0
votes
0
replies
1.1k
views
[R] Need to build package for Affy HT HG-U133+ PM arrays
Annotation
GO
cdf
probe
affy
pdInfoBuilder
Annotation
GO
cdf
probe
affy
pdInfoBuilder
15.2 years ago
James W. MacDonald
65k
0
votes
3
replies
1.6k
views
Problem with RMA using pdInfoBuilder, oligo and limma
cdf
probe
affy
limma
pdInfoBuilder
cdf
probe
affy
limma
pdInfoBuilder
15.3 years ago
Anne-Marie Madore
▴ 30
0
votes
2
replies
1.6k
views
Custom CDF files
Annotation
GO
cdf
affy
PROcess
oligo
pdInfoBuilder
Annotation
GO
cdf
affy
PROcess
updated 15.4 years ago by
Mark Robinson
★ 1.1k • written 15.4 years ago by
Edward Oakeley
▴ 20
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Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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