Showing : geo • reset
5
votes
12
replies
2.6k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 5.7 years ago by 21k • written 5.7 years ago by ▴ 20
3
votes
11
replies
4.0k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 6.3 years ago by 21k • written 7.1 years ago by • 0
1
vote
10
replies
452
views
Obtaining pheno data from CEL files
GEO affy
4 weeks ago • updated 25 days ago Kurtis • 0
10
votes
7
replies
2.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 60
6
votes
7
replies
2.2k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 50
5
votes
7
replies
2.1k
views
GEO series matrix empty
GEOquery GEO
2.2 years ago gs.123 ▴ 20
5
votes
7
replies
2.0k
views
what conditions affect my gene (with limma?)
limma geo experimental design
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
2
votes
6
replies
1.5k
views
error reading GSE using getGEO()
r geo getgeo
5.8 years ago jaleh.amo • 0
0
votes
6
replies
1.3k
views
Opening Illumina HT12 V3.0 Data from GEO
limma normalization GEO
4.6 years ago FL512 • 0
3
votes
6
replies
2.9k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.0 years ago andy_shaps ▴ 10
5
votes
5
replies
2.5k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 10
6
votes
5
replies
1.3k
views
a problem of package ""
GEO GEOquery
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 20
1
vote
5
replies
1.1k
views
Can't read in CEL files
GEO GEOquery
22 months ago OE • 0
0
votes
5
replies
1.9k
views
collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 8.4 years ago by ★ 3.3k • written 8.4 years ago by • 0
4
votes
5
replies
1.4k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 40
3
votes
5
replies
5.0k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
6.3 years ago martinguerrerog89 ▴ 20
2
votes
4
replies
1.6k
views
read bead-level data directly by lumi
bead-level GEO lumi
updated 8.2 years ago by ★ 6.5k • written 8.2 years ago by • 0
0
votes
4
replies
1.5k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 5.9 years ago by 21k • written 5.9 years ago by ▴ 10
1
vote
4
replies
1.2k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel GEO gene-expression
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
1
vote
3
replies
937
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 5.7 years ago by 65k • written 5.7 years ago by ▴ 20
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 50k • written 6.5 years ago by • 0
1
vote
3
replies
1.4k
views
Getting gene annotation for a GEO dataset
geo
6.8 years ago yuvallb • 0
2
votes
3
replies
992
views
Problem about Geoquery
GEO GEOquery
2.9 years ago sheldon19931016 ▴ 20
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
1
vote
2
replies
1.7k
views
Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from …
limma microarray agilent microarrays GEO
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
2
replies
882
views
Annotation Using GEOquery
Annotation GEO TXT
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
2
votes
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by ▴ 10
2
votes
2
replies
2.1k
views
GEOquery error in downloading SOFT files
geoquery getgeo GEO
7.4 years ago hzc363 ▴ 20
1
vote
2
replies
2.4k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 10
3
votes
2
replies
1.4k
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb GEO R bioconductor
updated 5.8 years ago by 21k • written 5.8 years ago by ▴ 20
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 ★ 6.5k • written 8.2 years ago by • 0
4
votes
2
replies
1.3k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
3
votes
2
replies
1.1k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart geo software error ensembl
updated 4.9 years ago by ★ 6.5k • written 4.9 years ago by ▴ 10
0
votes
1
reply
1.1k
views
data handling from GSE22216 to exprSet object
GEO
updated 8.3 years ago by ★ 6.5k • written 8.3 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 8.5 years ago by 65k • written 8.5 years ago by • 0
1
vote
1
reply
1.3k
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 6.2 years ago by 21k • written 6.2 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 30
0
votes
1
reply
1.1k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by • 0
2
votes
1
reply
2.8k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
GEOquery download error
geoquery error message GEOquery GSE GEO
6.7 years ago Barah ▴ 20
0
votes
1
reply
530
views
how to solve this error
DESeq2 GEO miRNAData
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
0
replies
953
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
5.9 years ago daniel.green • 0
0
votes
0
replies
723
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
3.6 years ago andrade4beatriz • 0
46 results • Page 1 of 1
Recent ...
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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