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lumi
•
reset
0
votes
2
replies
2.5k
views
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
RSQLite
lumi
3.5 years ago
Rohmatul
• 0
6
votes
3
replies
1.4k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 3.9 years ago by
Sean Davis
21k • written 3.9 years ago by
fabian
▴ 40
2
votes
1
reply
988
views
lumi: Importing Methylation EPIC IDAT files
lumi
EPIC
Methylation
4.0 years ago
Zach Roe
▴ 10
0
votes
0
replies
879
views
lumi / RSQLite warning
lumi
4.2 years ago
stewart999
▴ 10
1
vote
4
replies
1.7k
views
download data from GEO Illumina platform
lumi
illumina human ht-12 v4
updated 5.4 years ago by
lhuang7
▴ 50 • written 5.4 years ago by
kankejia0703
• 0
1
vote
2
replies
1.5k
views
lumi package fails to load because of a missing dependency (bumphunter)
lumi
methylumi
updated 5.5 years ago by
lhuang7
▴ 50 • written 5.5 years ago by
kaur.alasoo
▴ 30
1
vote
4
replies
1.8k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
Alexander Azarian
▴ 30
2
votes
5
replies
2.3k
views
Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
limma
lumi
illumina
gene expression data
updated 2.4 years ago by
mohammedtoufiq91
▴ 10 • written 5.9 years ago by
Harpreet Kaur
• 0
0
votes
1
reply
1.3k
views
Analysing microarray raw data: GSEXXXX_non-normalized.txt
lumi
microarray
GSE
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
mkd12
• 0
2
votes
4
replies
2.7k
views
Problem in installing Bioconductor packages due to "IRanges"
lumi
methylumi
methyAnalysis
6.3 years ago
topijush
▴ 10
1
vote
3
replies
2.4k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
aaronrosenstein
• 0
0
votes
1
reply
1.2k
views
Add gene information to most expressed gene list (packages lumi and GOstats)
annotation
lumi
GOstats
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
marongiu.luigi
• 0
0
votes
0
replies
1.3k
views
Can't get the lumi and methylumi packages to work.
lumi
methylumi
7.0 years ago
gitteba
• 0
0
votes
0
replies
2.5k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
7.0 years ago
hkarakurt
▴ 20
2
votes
1
reply
1.4k
views
Differential Expression Analysis
differential gene expression
microarray
lumi
illumina
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
paul.elliot1994
• 0
1
vote
10
replies
3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi
lumi
methylumi
dmrcate
illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by
Tim Peters
▴ 180 • written 7.1 years ago by
poojitha.stemcell
▴ 10
1
vote
6
replies
1.9k
views
minfi and lumi not available for version 3.3.2
minfi
lumi
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Jessie.Johnson
▴ 10
0
votes
1
reply
1.3k
views
Problems in using lumi for importing illumina raw data
beadarray
lumi
normalization
microarray
illumina
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
Biologist
▴ 110
4
votes
5
replies
1.8k
views
Can't install 'lumi'
lumi
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
stewart999
▴ 10
0
votes
1
reply
1.2k
views
Annotation for Mouse Illumina Expression Chip V6.1.1
bead chip
Annotation
Mouse
Lumi
probeID2nuID
updated 7.8 years ago by
Andy Lynch
▴ 120 • written 7.8 years ago by
smt8n
• 0
0
votes
2
replies
1.3k
views
lumi: how to get number of beads information?
lumi
minfi
updated 7.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.8 years ago by
krishna312
• 0
0
votes
0
replies
1.0k
views
Lumi Control Data
lumi
illumina
microarray
8.0 years ago
m.a.bentley
• 0
0
votes
1
reply
1.1k
views
Lumi error in importMethylIDAT
lumi
methylation
illumina
updated 8.0 years ago by
James W. MacDonald
65k • written 8.0 years ago by
rasii
• 0
1
vote
2
replies
2.0k
views
Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
limma
lumi
illuminaio
illimina 450k methylation
microarray
8.1 years ago
Adam
• 0
2
votes
4
replies
1.6k
views
read bead-level data directly by lumi
bead-level
GEO
lumi
updated 8.2 years ago by
Mike Smith
★ 6.5k • written 8.2 years ago by
gnilihzeux
• 0
1
vote
2
replies
1.4k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 8.2 years ago by
Mike Smith
★ 6.5k • written 8.2 years ago by
gnilihzeux
• 0
1
vote
2
replies
2.1k
views
unable to find Lumi package in R
lumi
updated 8.2 years ago by
Steve Lianoglou
★ 13k • written 8.2 years ago by
nayeli0126
• 0
0
votes
4
replies
2.8k
views
Illumina ID Mapping library
lumi
illumina beadarray
microarray
8.2 years ago
kritikamish99
▴ 10
0
votes
2
replies
1.4k
views
Ilumina microarray gene expression
microarray
lumi
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 years ago by
kritikamish99
▴ 10
3
votes
12
replies
6.2k
views
packages installation problem
limma
Rqc
beadarray
Lumi
updated 8.2 years ago by
Welliton de Souza
▴ 70 • written 8.2 years ago by
raya.girish
• 0
0
votes
0
replies
1.2k
views
Question about lumiT warning message
lumi
8.4 years ago
clevy
▴ 10
0
votes
0
replies
903
views
"Error: object 'nuID' not found" error when using `returnAllMatches=TRUE` in `IlluminaID2nuID()`
lumi
lumihumanidmapping
8.5 years ago
aush
▴ 40
0
votes
0
replies
1.0k
views
no chip information in lumiHumanIDMapping?
lumi
lumihumanidmapping
8.5 years ago
aush
▴ 40
0
votes
0
replies
1.7k
views
Error in the Illumina ID to Gene Symbol mapping through lumi package
lumi
illuminahumanv3
lumihumanidmapping
8.8 years ago
gokcen.eraslan
▴ 10
2
votes
2
replies
2.0k
views
Lumi - Can't write to pData Slot
lumi
updated 8.8 years ago by
Martin Morgan
25k • written 8.8 years ago by
andrew.j.skelton73
▴ 370
2
votes
8
replies
3.6k
views
Problems importing Illumina raw data with lumi R package
Illumina Human HT-12 v4
lumi
limma
microarray
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
svlachavas
▴ 830
1
vote
3
replies
1.8k
views
lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0
lumi
9.0 years ago
Jeremy Martinson
• 0
2
votes
7
replies
2.6k
views
Removing samples from S4 object (in lumi)
lumi
S4
9.2 years ago
Chi Hong
• 0
0
votes
1
reply
1.2k
views
lumi: can't see sample corr pairwise and MAplot plots
lumi
plot
updated 9.2 years ago by
Gordon Smyth
50k • written 9.3 years ago by
Frederico Moraes Ferreira
▴ 100
0
votes
2
replies
1.5k
views
lumiHumanIDMapping/lumiHumanAll for R-3.1.2
lumi
lumiHumanIDMapping
lumiHumanAll
9.3 years ago
Frederico Moraes Ferreira
▴ 100
0
votes
1
reply
925
views
Issues with lumi package
lumi
9.4 years ago
Sylvain Foisy
▴ 80
2
votes
20
replies
10k
views
problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
lumi
updated 9.0 years ago by
laseaman
• 0 • written 9.5 years ago by
lucashusquin
▴ 10
0
votes
1
reply
1.8k
views
how to set up sampleInfo for methylation array in illumina 450K
lumi
lumi
updated 10.0 years ago by
Pan Du
▴ 440 • written 10.0 years ago by
Guest User
★ 13k
1
vote
1
reply
1.8k
views
Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?
Normalization
probe
lumi
Normalization
probe
lumi
updated 9.3 years ago by
dsweeney
• 0 • written 10.2 years ago by
Nick Fishbane
▴ 20
0
votes
5
replies
2.0k
views
Coercion lumi/minfi objects
lumi
minfi
lumi
minfi
updated 10.2 years ago by
Tim Triche
★ 4.2k • written 10.2 years ago by
Aileen Bahl
▴ 10
0
votes
0
replies
1.5k
views
EximiR - Limma - miRCURY LNA - Exiqon
miRNA
Microarray
Cancer
limma
lumi
ExiMiR
miRNA
Microarray
Cancer
limma
lumi
ExiMiR
10.3 years ago
Paolo Kunderfranco
▴ 350
0
votes
0
replies
1.8k
views
Illumina Expression analysis from iDAT files
Normalization
limma
beadarray
lumi
illuminaio
Normalization
limma
beadarray
lumi
10.4 years ago
Kasper Daniel Hansen
★ 6.5k
3
votes
9
replies
5.7k
views
Illumina Expression analysis from iDAT files
beadarray
lumi
illuminaio
idat
updated 2.4 years ago by
Gordon Smyth
50k • written 10.4 years ago by
Sean Davis
21k
0
votes
2
replies
4.4k
views
Annotate - gene name to ENSEMBL
Microarray
GO
lumi
Microarray
GO
lumi
updated 10.5 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 10.5 years ago by
Kripa R
▴ 180
0
votes
10
replies
2.2k
views
MethyLumiM to MethyLumiSet?
convert
lumi
methylumi
minfi
wateRmelon
convert
lumi
methylumi
minfi
wateRmelon
updated 10.5 years ago by
Tim Triche
★ 4.2k • written 10.5 years ago by
Martin Rijlaarsdam
▴ 190
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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