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Illumina
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18
votes
37
replies
16k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
8.9 years ago • updated 8.8 years ago
svlachavas
▴ 830
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 8.6 years ago by
Mark Cowley
▴ 400 • written 8.6 years ago by
willj
▴ 30
7
votes
4
replies
1.6k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
Jason
▴ 20
6
votes
9
replies
1.5k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma
illumina
microarray
multifactorial design
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Konstantinos Yeles
▴ 80
4
votes
2
replies
4.6k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
Li Liu
▴ 100
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
kritikamish99
▴ 10
4
votes
5
replies
2.9k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 8.9 years ago by
svlachavas
▴ 830 • written 8.9 years ago by
Agaz Hussain Wani
▴ 260
3
votes
6
replies
2.4k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma
illumina
microarray
lmfit
differential gene expression
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
kanacska
▴ 10
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.1 years ago
rasii
• 0
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 5.8 years ago by
Harpreet Kaur
• 0
2
votes
1
reply
1.5k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina
bioconductor
limma
microarray
normalization
updated 8.4 years ago by
Gordon Smyth
50k • written 8.5 years ago by
Konstantinos Yeles
▴ 80
2
votes
4
replies
1.6k
views
read.idat function misleading error when reading compressed files
idat
illumina
limma
read.idat
updated 3.3 years ago by
Gordon Smyth
50k • written 3.4 years ago by
bastien_chassagnol
• 0
2
votes
3
replies
1.6k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
Stane
▴ 40
2
votes
4
replies
1.3k
views
The error when using beadarry and limma packages for analysing illumina chip
limma
beadarray
illumina
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
261092095
▴ 10
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
2
votes
2
replies
1.6k
views
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
illumina human ht-12 v4
illuminahumanv4.db
filtering on probe annotation
illumina
updated 8.9 years ago by
Mike Smith
★ 6.5k • written 8.9 years ago by
svlachavas
▴ 830
2
votes
3
replies
2.5k
views
Normalization of Illumina Microarray Data
illumina
microarray
normalization
updated 7.1 years ago by
Gordon Smyth
50k • written 7.1 years ago by
paul.elliot1994
• 0
1
vote
1
reply
936
views
PCA input data from DRAGEN RNA pipeline
illumina
PCAtools
PCA
updated 17 months ago by
Kevin Blighe
★ 3.9k • written 17 months ago by
ilaria.debenedictis
• 0
1
vote
6
replies
2.1k
views
Copy number analysis from Illumina 550K chip
illumina
copynumber
crlmm
8.5 years ago
stuti.agrawal
• 0
1
vote
1
reply
1.3k
views
Error genotyping with CRLMM
crlmm
copynumber
illumina
updated 8.5 years ago by
andrew.j.skelton73
▴ 370 • written 8.5 years ago by
stuti.agrawal
• 0
1
vote
5
replies
1.9k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm
illumina
beadarraysnp
updated 9.1 years ago by
Matthew Ritchie
▴ 1000 • written 9.2 years ago by
René
▴ 30
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi
methylation
illumina
9.5 years ago
Brian Smith
▴ 120
1
vote
3
replies
1.4k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
6.8 years ago
ezrabekele17
• 0
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
kelvinfrog75
• 0
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.4 years ago by
k.vitting.seerup
▴ 120 • written 6.4 years ago by
amy16
• 0
1
vote
5
replies
1.2k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2
rna-seq
illumina
batch effect
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
JP Carter
▴ 40
1
vote
1
reply
1.4k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm
gsa
microarray
illumina
written 6.0 years ago by
shaun
• 0
1
vote
1
reply
1.7k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names
methylation
illumina
convertids
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
arbet003
▴ 10
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
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 5.4 years ago by
Ou, Jianhong
★ 1.3k • written 5.4 years ago by
Adam_M
• 0
1
vote
3
replies
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.2 years ago
erwin.tomasich
▴ 10
1
vote
14
replies
3.7k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools
qualitycontrol
HumanOmni5-4BeadChip
GenomeStudio
illumina
updated 8.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 8.0 years ago by
Lna
• 0
1
vote
4
replies
438
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
11 weeks ago
mikat
• 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 6.0 years ago by
James W. MacDonald
65k • written 6.1 years ago by
amy16
• 0
0
votes
2
replies
1.1k
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 6.0 years ago by
ta_awwad
▴ 10 • written 6.0 years ago by
soheilazareie
• 0
0
votes
7
replies
2.0k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 5.0 years ago by
Guido Hooiveld
★ 3.9k • written 5.0 years ago by
naf
• 0
0
votes
2
replies
866
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
3.2 years ago
sissialva21
• 0
0
votes
0
replies
896
views
Annotation Illumina Infinium Mouse Methylation
Illumina
minfi
IlluminaHumanMethylationEPICmanifest
2.0 years ago
octaviompa
• 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
0
votes
2
replies
1.9k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi
minfidata
illumina
methylation
dmpfinder
updated 9.6 years ago by
James W. MacDonald
65k • written 9.6 years ago by
michael.zulyniak
• 0
0
votes
6
replies
2.2k
views
Illumina bead array analysis
illumina
beadarray
updated 14 months ago by
Mark Dunning
★ 1.1k • written 9.6 years ago by
tomiptu
• 0
0
votes
6
replies
1.3k
views
Getting CDS positioning for IlluminaHumanv4 annotations
illumina
annotation
9.4 years ago
Sylvain Foisy
▴ 80
0
votes
1
reply
1.6k
views
Error regarding installation and loading of "Lumi" Package
software error
microarray
illumina
updated 9.3 years ago by
Steve Lianoglou
★ 13k • written 9.3 years ago by
Deeksha Malhan
▴ 10
0
votes
0
replies
1.7k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray
beadarray
Illumina
Veracode
9.2 years ago
lacion
• 0
0
votes
7
replies
1.6k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 9.1 years ago by
Mike Smith
★ 6.5k • written 9.1 years ago by
harpreet.saini
• 0
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread
illumina
9.1 years ago
danova_fr
▴ 20
0
votes
2
replies
5.3k
views
How to read bgx files in R
microarray
annotation
illumina
8.8 years ago
kanacska
▴ 10
0
votes
6
replies
4.0k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina
normalization
microarray
updated 8.8 years ago by
Mark Dunning
★ 1.1k • written 8.8 years ago by
kanacska
▴ 10
0
votes
0
replies
1.1k
views
WG6 microarray version 2 and 3, reading in txt file from two platforms
limma
illumina
microarray
normalization
readillumina
8.7 years ago
kanacska
▴ 10
0
votes
0
replies
1.4k
views
minfi v1.14 through champ: read.450k error with file path name
minfi
champ
illumina
450k
8.7 years ago
jeroen
• 0
50 results • Page
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Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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