Showing : Illumina • reset
0
votes
2
replies
260
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
7 months ago sissialva21 • 0
2
votes
4
replies
336
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 8 months ago by 43k • written 9 months ago by • 0
1
vote
3
replies
279
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
19 months ago erwin.tomasich ▴ 10
0
votes
7
replies
535
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 2.4 years ago by ★ 3.0k • written 2.4 years ago by • 0
1
vote
2
replies
600
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.8 years ago by ★ 1.2k • written 2.8 years ago by • 0
1
vote
4
replies
904
views
Trouble loading 'lumi' package
lumi illumina hdf5array
updated 3.1 years ago by 58k • written 3.1 years ago by ▴ 20
0
votes
2
replies
629
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 3.2 years ago by 43k • written 3.2 years ago by • 0
2
votes
4
replies
508
views
The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
1
vote
1
reply
765
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 3.3 years ago by 58k • written 3.3 years ago by ▴ 10
1
vote
1
reply
619
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
1
vote
5
replies
539
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 3.4 years ago by 34k • written 3.4 years ago by ▴ 40
0
votes
2
replies
445
views
BAM file into R from Illumina
bam file STAR Illumina
updated 3.4 years ago by ▴ 10 • written 3.4 years ago by • 0
0
votes
3
replies
900
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 3.4 years ago by 58k • written 3.4 years ago by • 0
1
vote
1
reply
604
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 3.8 years ago by ▴ 100 • written 3.8 years ago by • 0
0
votes
3
replies
987
views
How can I pre-process illumina raw file
illumina microarray
updated 4.1 years ago by 58k • written 4.1 years ago by ▴ 260
1
vote
3
replies
770
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
4.2 years ago ezrabekele17 • 0
0
votes
0
replies
519
views
minfi error with dmpfinder
methylation illumina
4.3 years ago indranipoddar • 0
0
votes
2
replies
953
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by • 0
0
votes
0
replies
1.4k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi illumina normalization beadarray
4.4 years ago hkarakurt ▴ 20
2
votes
1
reply
860
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 4.5 years ago by 58k • written 4.5 years ago by • 0
2
votes
3
replies
1.6k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
3
replies
808
views
MINFI missing samples in qcreports and densityplots
minfi illumina methylationEPIC densityplot
4.7 years ago annabelle.congras ▴ 10
0
votes
1
reply
623
views
Problems in using lumi for importing illumina raw data
beadarray lumi normalization microarray illumina
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 90
0
votes
4
replies
997
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
updated 5.0 years ago by • 0 • written 5.1 years ago by • 0
0
votes
0
replies
799
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads methylation illumina epic microarray
5.1 years ago rasii • 0
2
votes
3
replies
972
views
lumiR [Illumina] error from non-normalized data
illumina
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 40
0
votes
0
replies
681
views
Illumina Genotyping in parallel raise an error
crlmm snp illumina
5.2 years ago nadne ▴ 10
6
votes
9
replies
872
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 5.2 years ago by 43k • written 5.2 years ago by ▴ 70
0
votes
1
reply
1.2k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
0
votes
2
replies
602
views
permutation with plink
illumina plink permutation
updated 5.3 years ago by 58k • written 5.3 years ago by • 0
0
votes
0
replies
546
views
Lumi Control Data
lumi illumina microarray
5.4 years ago m.a.bentley • 0
1
vote
14
replies
2.2k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 5.4 years ago by ▴ 800 • written 5.4 years ago by • 0
0
votes
1
reply
684
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 5.4 years ago by 58k • written 5.4 years ago by • 0
0
votes
1
reply
1.0k
views
Error in Matrix
minfi methylation EPIC microarray illumina
updated 5.4 years ago by 6.5k • written 5.4 years ago by • 0
3
votes
15
replies
2.8k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
5.4 years ago rasii • 0
0
votes
4
replies
802
views
minfi sample limit
minfi illumina illimina 450k methylation methylation
updated 5.5 years ago by 6.5k • written 5.5 years ago by ▴ 40
0
votes
3
replies
1.1k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 110
0
votes
2
replies
822
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
5.6 years ago kritikamish99 ▴ 10
4
votes
8
replies
5.1k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
0
votes
0
replies
896
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
5.6 years ago walter_teng • 0
7
votes
4
replies
915
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 5.7 years ago by 58k • written 5.7 years ago by ▴ 20
0
votes
0
replies
824
views
Repetitive motifs on Illumina 450k derived sequences
illumina 450k motifs meme
5.7 years ago Gustavo Fernández Bayón ▴ 440
0
votes
0
replies
580
views
Problems using the savR package
savR illumina
5.7 years ago merella.stefania • 0
1
vote
1
reply
976
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 70
1
vote
6
replies
1.2k
views
Copy number analysis from Illumina 550K chip
illumina copynumber crlmm
5.9 years ago stuti.agrawal • 0
1
vote
1
reply
772
views
Error genotyping with CRLMM
crlmm copynumber illumina
updated 5.9 years ago by ▴ 340 • written 5.9 years ago by • 0
0
votes
4
replies
1.6k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina annotation
updated 5.9 years ago by ★ 5.1k • written 5.9 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray illumina methylation microarray
updated 6.0 years ago by 21k • written 6.0 years ago by • 0
11
votes
5
replies
1.5k
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 6.0 years ago by ▴ 400 • written 6.0 years ago by ▴ 30
0
votes
0
replies
1.0k
views
minfi v1.14 through champ: read.450k error with file path name
minfi champ illumina 450k
6.1 years ago jeroen • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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