Showing : illumina • reset
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
9.6 years ago • updated 9.5 years ago svlachavas ▴ 840
11
votes
5
replies
2.6k
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 9.3 years ago by ▴ 400 • written 9.3 years ago by ▴ 30
7
votes
4
replies
1.8k
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 9.0 years ago by 67k • written 9.0 years ago by ▴ 20
6
votes
9
replies
1.8k
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 8.6 years ago by 52k • written 8.6 years ago by ▴ 80
4
votes
2
replies
5.0k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 100
4
votes
5
replies
3.1k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina pvalue
updated 9.6 years ago by ▴ 840 • written 9.6 years ago by ▴ 260
4
votes
8
replies
11k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 10
3
votes
15
replies
4.9k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.8 years ago rasii • 0
3
votes
6
replies
2.8k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma illumina microarray lmfit differential gene expression
updated 9.4 years ago by 67k • written 9.4 years ago by ▴ 10
3
votes
14
replies
4.2k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 8.7 years ago by ▴ 890 • written 8.7 years ago by • 0
2
votes
4
replies
2.0k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 4.1 years ago by 52k • written 4.1 years ago by • 0
2
votes
3
replies
2.8k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 7.8 years ago by 52k • written 7.8 years ago by • 0
2
votes
5
replies
2.8k
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 3.1 years ago by ▴ 10 • written 6.6 years ago by • 0
2
votes
3
replies
1.7k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 8.4 years ago by 52k • written 8.4 years ago by ▴ 40
2
votes
2
replies
1.8k
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 9.6 years ago by ★ 6.6k • written 9.6 years ago by ▴ 840
2
votes
4
replies
1.5k
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 6.6 years ago by 52k • written 6.6 years ago by ▴ 10
2
votes
1
reply
1.7k
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 7.8 years ago by 67k • written 7.8 years ago by • 0
2
votes
1
reply
1.7k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 9.2 years ago by 52k • written 9.2 years ago by ▴ 80
1
vote
1
reply
1.4k
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
1
vote
6
replies
2.4k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
9.2 years ago stuti.agrawal • 0
1
vote
1
reply
1.5k
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 9.2 years ago by ▴ 370 • written 9.2 years ago by • 0
1
vote
5
replies
2.1k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm illumina beadarraysnp
updated 9.9 years ago by ▴ 1000 • written 9.9 years ago by ▴ 30
1
vote
2
replies
1.7k
views
minfi package QC report error?
minfi methylation illumina
10.2 years ago Brian Smith ▴ 120
1
vote
3
replies
1.7k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
7.5 years ago ezrabekele17 • 0
1
vote
7
replies
6.3k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.8 years ago by 25k • written 9.8 years ago by • 0
1
vote
1
reply
1.6k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 7.2 years ago by ▴ 120 • written 7.2 years ago by • 0
1
vote
5
replies
1.4k
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 6.7 years ago by 43k • written 6.7 years ago by ▴ 40
1
vote
1
reply
1.7k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
written 6.7 years ago by • 0
1
vote
1
reply
2.1k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 6.7 years ago by 67k • written 6.7 years ago by ▴ 10
1
vote
4
replies
2.2k
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 6.4 years ago by 67k • written 6.4 years ago by ▴ 30
1
vote
2
replies
1.6k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 6.1 years ago by ★ 1.3k • written 6.1 years ago by • 0
1
vote
3
replies
1.7k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
5.0 years ago erwin.tomasich ▴ 10
1
vote
4
replies
1.1k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 months ago mikat • 0
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.8 years ago by 67k • written 6.8 years ago by • 0
0
votes
2
replies
1.3k
views
BAM file into R from Illumina
bam file STAR Illumina
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
0
votes
7
replies
2.4k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 5.7 years ago by ★ 4.1k • written 5.7 years ago by • 0
0
votes
2
replies
1.1k
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.0 years ago sissialva21 • 0
0
votes
0
replies
1.2k
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.7 years ago octaviompa • 0
0
votes
1
reply
1.3k
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 8.7 years ago by 67k • written 8.7 years ago by • 0
0
votes
2
replies
2.2k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi minfidata illumina methylation dmpfinder
updated 10.3 years ago by 67k • written 10.3 years ago by • 0
0
votes
6
replies
2.4k
views
Illumina bead array analysis
illumina beadarray
updated 22 months ago by ★ 1.1k • written 10.3 years ago by • 0
0
votes
6
replies
1.4k
views
Getting CDS positioning for IlluminaHumanv4 annotations
illumina annotation
10.1 years ago Sylvain Foisy ▴ 80
0
votes
1
reply
1.8k
views
Error regarding installation and loading of "Lumi" Package
software error microarray illumina
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray beadarray Illumina Veracode
10.0 years ago lacion • 0
0
votes
7
replies
1.9k
views
getting error in processSwathData command from the beadarray package
microarray beadarray illumina
updated 9.8 years ago by ★ 6.6k • written 9.8 years ago by • 0
0
votes
2
replies
1.5k
views
ShortRead summary stats
shortread illumina
9.8 years ago danova_fr ▴ 20
0
votes
2
replies
5.9k
views
How to read bgx files in R
microarray annotation illumina
9.5 years ago kanacska ▴ 10
0
votes
6
replies
4.5k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina normalization microarray
updated 9.5 years ago by ★ 1.1k • written 9.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
WG6 microarray version 2 and 3, reading in txt file from two platforms
limma illumina microarray normalization readillumina
9.4 years ago kanacska ▴ 10
0
votes
0
replies
1.5k
views
minfi v1.14 through champ: read.450k error with file path name
minfi champ illumina 450k
9.4 years ago jeroen • 0
50 results • Page 1 of 1
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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