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
9.0 years ago • updated 8.8 years ago svlachavas ▴ 830
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.1 years ago rasii • 0
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 ▴ 870 • written 8.0 years ago by • 0
6
votes
9
replies
1.6k
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 7.9 years ago by 50k • written 7.9 years ago by ▴ 80
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 8.3 years ago by 50k • written 8.3 years ago by ▴ 10
1
vote
7
replies
6.0k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.2 years ago by 25k • written 9.2 years ago by • 0
0
votes
7
replies
1.6k
views
getting error in processSwathData command from the beadarray package
microarray beadarray illumina
updated 9.2 years ago by ★ 6.5k • written 9.2 years ago by • 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 ★ 4.0k • written 5.0 years ago by • 0
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 8.8 years ago by 66k • written 8.8 years ago by ▴ 10
1
vote
6
replies
2.1k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
8.6 years ago stuti.agrawal • 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
6
replies
2.2k
views
Illumina bead array analysis
illumina beadarray
updated 15 months ago by ★ 1.1k • written 9.6 years ago by • 0
0
votes
6
replies
4.0k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina normalization microarray
updated 8.9 years ago by ★ 1.1k • written 8.9 years ago by ▴ 10
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 6.1 years ago by 42k • written 6.1 years ago by ▴ 40
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 ▴ 830 • written 8.9 years ago by ▴ 260
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 ▴ 10 • written 5.9 years ago by • 0
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 8.7 years ago by ▴ 400 • written 8.7 years ago by ▴ 30
1
vote
5
replies
1.9k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm illumina beadarraysnp
updated 9.2 years ago by ▴ 1000 • written 9.2 years ago by ▴ 30
1
vote
4
replies
1.8k
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 5.8 years ago by 66k • written 5.8 years ago by ▴ 30
2
votes
4
replies
1.3k
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 10
1
vote
4
replies
529
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
3 months ago mikat • 0
0
votes
4
replies
2.4k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 8.6 years ago by ★ 6.5k • written 8.6 years ago by ▴ 10
2
votes
4
replies
1.6k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
votes
4
replies
1.6k
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 8.2 years ago by ★ 6.5k • written 8.2 years ago by ▴ 50
0
votes
4
replies
1.9k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
updated 7.7 years ago by • 0 • written 7.8 years ago by • 0
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 66k • written 8.3 years ago by ▴ 20
2
votes
3
replies
1.6k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 40
1
vote
3
replies
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.3 years ago erwin.tomasich ▴ 10
0
votes
3
replies
2.2k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 8.3 years ago by 50k • written 8.3 years ago by ▴ 110
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.1 years ago by 66k • written 6.1 years ago by • 0
0
votes
3
replies
1.5k
views
How can I pre-process illumina raw file
illumina microarray
updated 6.8 years ago by 66k • written 6.8 years ago by ▴ 260
1
vote
3
replies
1.5k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
6.9 years ago ezrabekele17 • 0
2
votes
3
replies
2.5k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
0
votes
3
replies
1.6k
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
7.4 years ago annabelle.congras ▴ 10
0
votes
2
replies
1.1k
views
BAM file into R from Illumina
bam file STAR Illumina
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
4
votes
2
replies
4.6k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 9.5 years ago by 66k • written 9.6 years ago by ▴ 100
0
votes
2
replies
1.8k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray illumina methylation microarray
updated 8.6 years ago by 21k • written 8.6 years ago by • 0
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 ★ 1.3k • written 5.4 years ago by • 0
0
votes
2
replies
1.2k
views
permutation with plink
illumina plink permutation
updated 8.0 years ago by 66k • written 8.0 years ago by • 0
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi methylation illumina
9.6 years ago Brian Smith ▴ 120
0
votes
2
replies
887
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
3.3 years ago sissialva21 • 0
0
votes
2
replies
5.4k
views
How to read bgx files in R
microarray annotation illumina
8.9 years ago kanacska ▴ 10
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 9.0 years ago by ★ 6.5k • written 9.0 years ago by ▴ 830
0
votes
2
replies
1.3k
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
8.3 years ago kritikamish99 ▴ 10
0
votes
2
replies
1.9k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi minfidata illumina methylation dmpfinder
updated 9.7 years ago by 66k • written 9.7 years ago by • 0
0
votes
2
replies
1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 7.0 years ago by ★ 4.0k • written 7.0 years ago by • 0
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread illumina
9.2 years ago danova_fr ▴ 20
1
vote
1
reply
986
views
PCA input data from DRAGEN RNA pipeline
illumina PCAtools PCA
updated 18 months ago by ★ 3.9k • written 18 months ago by • 0
0
votes
1
reply
1.6k
views
Error regarding installation and loading of "Lumi" Package
software error microarray illumina
updated 9.4 years ago by ★ 13k • written 9.4 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 8.6 years ago by ▴ 370 • written 8.6 years ago by • 0
50 results • Page 1 of 1
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Comment: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.1k
Hi, What do you get if you run the following `httr::HEAD()` command? I noticed that you have `libcurl` version 8.3.0 from `curl::curl_vers…
Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you @mikelove for your patience and kind advice. So I assume the plots from R are valid. Best wishes.
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Votes
Comment: recount3 problem downloading data from source sra
Answer: Slightly different count plots from R and spreadsheet
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
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