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probe
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reset
0
votes
0
replies
4.4k
views
Limma for DNA methylation arrays?
Normalization
probe
limma
minfi
Normalization
probe
limma
minfi
11.9 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
4
replies
2.8k
views
Limma, blocking, robust methods, and paired samples question
Microarray
probe
Microarray
probe
updated 11.9 years ago by
Gordon Smyth
53k • written 11.9 years ago by
Gustavo Fernández Bayón
▴ 440
0
votes
0
replies
1.4k
views
Questions regarding 'specond' r-program library package
Kidney
Lung
Prostate
probe
SpeCond
Kidney
Lung
Prostate
probe
SpeCond
11.9 years ago
Florence Cavalli
▴ 50
0
votes
3
replies
1.3k
views
Cross map two different probe set IDs
probe
probe
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
Jerry Cholo
▴ 190
0
votes
0
replies
1.7k
views
limma duplicateCorrelation - unbalanced paired design
probe
probe
12.0 years ago
sbcn
▴ 80
0
votes
0
replies
1.4k
views
Farms/Call.INI using oligo package?
probe
affy
oligo
SIM
farms
probe
affy
oligo
SIM
farms
12.0 years ago
Djork Clevert
▴ 210
3
votes
5
replies
2.1k
views
Farms/Call.INI using oligo package?
probe
affy
oligo
farms
probe
affy
oligo
farms
updated 12.0 years ago by
Djork Clevert
▴ 210 • written 12.0 years ago by
Fraser Sim
▴ 270
0
votes
1
reply
926
views
Probe Set IDs and Gene Names for Human Gene 1.1 ST array
probe
probe
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Shahla Ghaumipour
▴ 10
0
votes
3
replies
2.2k
views
Summarisation in oligo package after exclusion of probes containing SNPs
probe
affy
oligo
probe
affy
oligo
updated 12.0 years ago by
Daniel Bottomly
▴ 20 • written 12.0 years ago by
Guest User
★ 13k
0
votes
1
reply
2.6k
views
affy - Anotation of Afymetrix PrimeView chipe
cdf
probe
affy
limma
cdf
probe
affy
limma
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Adam Olejnik
▴ 10
0
votes
0
replies
986
views
Illumina spike-in probe sequences, lumi
Annotation
probe
Annotation
probe
12.1 years ago
Rohmatul Fajriyah
▴ 190
0
votes
2
replies
5.5k
views
Normalization before ComBat
Microarray
Normalization
probe
affy
frma
Microarray
Normalization
probe
affy
frma
updated 12.1 years ago by
francesco.brundu@gmail.com
▴ 40 • written 12.1 years ago by
W. Evan Johnson
▴ 870
0
votes
2
replies
1.9k
views
limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Annotation
Normalization
GO
probe
annotate
Annotation
Normalization
GO
probe
annotate
updated 12.1 years ago by
Wei Shi
★ 3.6k • written 12.1 years ago by
Kemal Akat
▴ 120
0
votes
0
replies
1.1k
views
variation between chips - neqc()
Microarray
Normalization
probe
limma
lumi
Microarray
Normalization
probe
limma
lumi
12.1 years ago
Rao,Xiayu
▴ 550
0
votes
0
replies
906
views
Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Annotation
probe
Annotation
probe
12.1 years ago
Nitesh Turaga
▴ 50
0
votes
2
replies
3.9k
views
topGO issues
Annotation
GO
probe
Annotation
GO
probe
updated 12.1 years ago by
Marc Carlson
★ 7.2k • written 12.2 years ago by
Guest User
★ 13k
0
votes
1
reply
1.6k
views
Error using makeDBPackage() from AnnotationForge package
Annotation
probe
AnnotationForge
Annotation
probe
AnnotationForge
updated 12.1 years ago by
Marc Carlson
★ 7.2k • written 12.1 years ago by
gabriel teku
▴ 80
0
votes
3
replies
4.1k
views
How to deal with Affymetrix probe that map to multiple genes
GO
Clustering
probe
convert
GO
Clustering
probe
convert
12.2 years ago
Gundala Viswanath
▴ 230
0
votes
0
replies
2.6k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH
RNASeq
ChIPSeq
Proteomics
Annotation
Normalization
GO
Network
Cancer
ChipName
probe
12.2 years ago
Sarah JugurnauthLittle
▴ 20
0
votes
0
replies
764
views
Error while background correction
GO
probe
GO
probe
12.2 years ago
kunal jha
▴ 10
0
votes
0
replies
2.5k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment
Annotation
Normalization
GO
Preprocessing
Clustering
Cancer
Organism
probe
GLAD
12.2 years ago
Sarah Pohl
▴ 30
0
votes
1
reply
2.5k
views
Control probe QC plots for Infinium 450k chips (lumi, minfi...)
Annotation
probe
lumi
minfi
Annotation
probe
lumi
minfi
updated 12.2 years ago by
Tim Triche
★ 4.2k • written 12.2 years ago by
Jon Manning
▴ 90
0
votes
2
replies
2.2k
views
Reading Illumina data from GenomeStudio in limma
probe
lumi
probe
lumi
updated 12.2 years ago by
Wei Shi
★ 3.6k • written 12.2 years ago by
Guest User
★ 13k
0
votes
1
reply
884
views
RMA probe summarization when sizes of probesets are unequal
Microarray
Normalization
probe
oligo
Microarray
Normalization
probe
oligo
updated 12.2 years ago by
James W. MacDonald
68k • written 12.2 years ago by
Guest User
★ 13k
0
votes
8
replies
3.3k
views
Affy: probeset to gene expression with expresso
probe
affy
probe
affy
updated 12.2 years ago by
James W. MacDonald
68k • written 12.2 years ago by
Martin Preusse
▴ 50
1
vote
4
replies
4.9k
views
[topGO] More flexible way to select 'interesting' genes
GO
probe
topGO
GO
probe
topGO
updated 12.2 years ago by
Adrian Alexa
▴ 400 • written 12.2 years ago by
enricoferrero
▴ 680
0
votes
0
replies
1.5k
views
CGHCall problems
aCGH
probe
DNAcopy
aCGH
CGHcall
aCGH
probe
DNAcopy
aCGH
CGHcall
12.3 years ago
Guest User
★ 13k
0
votes
2
replies
2.1k
views
Fwd: How to handle the case a Affymetrix probe set ID mapped to multiple genes?
Annotation
hgu133plus2
probe
Annotation
hgu133plus2
probe
updated 12.3 years ago by
Yuan Hao
▴ 240 • written 12.3 years ago by
Levi Waldron
★ 1.1k
0
votes
1
reply
916
views
issue on removing all NAs (UNANNOTATED) rows
probe
limma
probe
limma
updated 12.3 years ago by
James W. MacDonald
68k • written 12.3 years ago by
Guest User
★ 13k
0
votes
0
replies
815
views
Fwd: How to handle the case a Affymetrix probe set ID mapped to multiple genes?
Annotation
probe
Annotation
probe
12.3 years ago
Levi Waldron
★ 1.1k
0
votes
0
replies
846
views
How to handle the case a Affymetrix probe set ID mapped to multiple genes?
Annotation
probe
Annotation
probe
12.3 years ago
Feng Tian
▴ 110
0
votes
0
replies
889
views
maskBAD package - Errors during creation of mask
Microarray
probe
maskBAD
Microarray
probe
maskBAD
12.3 years ago
Ron Rotkopf
▴ 10
0
votes
4
replies
2.2k
views
DexSeq extracols option
RNASeq
Microarray
Genetics
Annotation
Normalization
Infrastructure
Cancer
probe
limma
updated 12.3 years ago by
Alejandro Reyes
★ 1.9k • written 12.3 years ago by
Ioannis Vlachos
▴ 40
0
votes
1
reply
627
views
Prolems with AraGene 1_1 annotation
Annotation
GO
cdf
probe
Annotation
GO
cdf
probe
updated 12.3 years ago by
James W. MacDonald
68k • written 12.3 years ago by
Hugh Shanahan
▴ 10
0
votes
2
replies
1.5k
views
limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray
Normalization
GO
Network
Cancer
probe
limma
Microarray
Normalization
GO
probe
updated 12.3 years ago by
Gordon Smyth
53k • written 12.3 years ago by
Peter Langfelder
★ 3.0k
0
votes
14
replies
3.9k
views
pd.hugene.2.0.st missing normgene->exon mappings
Cancer
probe
Cancer
probe
updated 12.3 years ago by
James W. MacDonald
68k • written 12.3 years ago by
Mark Cowley
▴ 910
0
votes
5
replies
2.0k
views
Illumina Probe_ID used in the LIMMA package for neqc function
Microarray
Annotation
Normalization
Clustering
probe
limma
Microarray
Annotation
probe
updated 12.3 years ago by
William D'Avigdor
▴ 40 • written 12.3 years ago by
Wei Shi
★ 3.6k
0
votes
2
replies
2.7k
views
Disparity between MethylLumiSet (methylumi) and RGChannelSet (minfi) - treatment of missing values
probe
methylumi
probe
methylumi
updated 12.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 12.3 years ago by
Pilling, Luke
▴ 20
0
votes
4
replies
1.9k
views
read.ilmn() and variation between chips
Microarray
Normalization
probe
limma
Microarray
Normalization
probe
limma
updated 12.3 years ago by
Gordon Smyth
53k • written 12.3 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
2.3k
views
Illumina Probe_ID used in the LIMMA package for neqc function
Microarray
Annotation
probe
limma
Microarray
Annotation
probe
limma
updated 12.3 years ago by
Wei Shi
★ 3.6k • written 12.3 years ago by
William D'Avigdor
▴ 40
0
votes
2
replies
2.4k
views
Question about mget vs. select for annotation package
hgu133plus2
probe
hgu133plus2
probe
updated 12.3 years ago by
Hervé Pagès
16k • written 12.3 years ago by
Christina Chaivorapol
▴ 40
0
votes
0
replies
740
views
sample probe profile or sample gene profile
Microarray
probe
Microarray
probe
12.4 years ago
Guest User
★ 13k
0
votes
0
replies
1.1k
views
illumina microarray analysis questions (limma and heatmap)
Microarray
Normalization
probe
limma
Microarray
Normalization
probe
limma
12.4 years ago
Rao,Xiayu
▴ 550
0
votes
4
replies
2.1k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray
Annotation
GO
Organism
probe
annotate
limma
convert
pdInfoBuilder
sva
GO
sva
updated 12.4 years ago by
Benilton Carvalho
★ 4.3k • written 12.4 years ago by
Johnson, Franklin Theodore
▴ 140
2
votes
4
replies
3.2k
views
makePdInfoPackage for Primeview arrays
BiocViews
Annotation
Cancer
Organism
cdf
probe
affy
biocViews
BiocViews
BiocViews
Cancer
updated 12.4 years ago by
cstrato
★ 3.9k • written 12.4 years ago by
Max Kauer
▴ 140
1
vote
4
replies
7.9k
views
How is LIMMA actually calculating the average expression value
probe
limma
gcrma
probe
limma
gcrma
updated 12.4 years ago by
Garcia Orellana,Miriam
▴ 150 • written 12.4 years ago by
Gordon Smyth
53k
0
votes
1
reply
826
views
could not find function "makeProbePackage"
cdf
probe
cdf
probe
updated 12.4 years ago by
James W. MacDonald
68k • written 12.4 years ago by
Merja Heinäniemi
▴ 10
0
votes
0
replies
1.1k
views
Error while executing ComBat from sva library in bioconductor
probe
sva
probe
sva
12.4 years ago
W. Evan Johnson
▴ 870
0
votes
2
replies
1.5k
views
first time using combat
probe
sva
probe
sva
updated 12.4 years ago by
Fernando Andrade
▴ 10 • written 12.4 years ago by
W. Evan Johnson
▴ 870
0
votes
1
reply
1.0k
views
using beadarray or limma without spatial information
Microarray
probe
Microarray
probe
updated 12.4 years ago by
Wei Shi
★ 3.6k • written 12.4 years ago by
Guest User
★ 13k
1,388 results • Page
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Replies
Answer: Integration: Paired-end vs healthy single-end from a different source
by
James W. MacDonald
68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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