Showing : geo • reset
4
votes
17
replies
5.7k
views
How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 5 months ago by ★ 5.0k • written 6 months ago by ▴ 10
0
votes
1
reply
584
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
3
replies
912
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
15 months ago gallantk5 • 0
0
votes
4
replies
1.4k
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 16 months ago by 21k • written 16 months ago by • 0
0
votes
9
replies
1.4k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
16 months ago gallantk5 • 0
1
vote
10
replies
1.9k
views
Obtaining pheno data from CEL files
GEO affy
19 months ago Kurtis • 0
0
votes
1
reply
1.0k
views
how to solve this error
DESeq2 GEO miRNAData
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
1
vote
5
replies
2.0k
views
Can't read in CEL files
GEO GEOquery
3.4 years ago OE • 0
5
votes
7
replies
3.5k
views
GEO series matrix empty
GEOquery GEO
3.7 years ago gs.123 ▴ 20
1
vote
2
replies
3.6k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.9 years ago by 21k • written 4.0 years ago by ▴ 10
6
votes
7
replies
3.4k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 50
1
vote
3
replies
1.7k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
6
votes
5
replies
1.9k
views
a problem of package ""
GEO GEOquery
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 20
2
votes
3
replies
1.7k
views
Problem about Geoquery
GEO GEOquery
4.5 years ago sheldon19931016 ▴ 20
4
votes
2
replies
1.8k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
3
votes
4
replies
2.2k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.6 years ago hgalmoore • 0
2
votes
1
reply
3.8k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
5
votes
5
replies
4.6k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
5.2 years ago andrade4beatriz • 0
2
votes
2
replies
2.8k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Table expression data from GEO file
GEO expression GEOquery
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by • 0
0
votes
1
reply
1.9k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
4
replies
1.8k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel GEO gene-expression
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
4
votes
5
replies
2.1k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.7 years ago by 53k • written 5.8 years ago by ▴ 40
0
votes
2
replies
1.4k
views
Annotation Using GEOquery
Annotation GEO TXT
updated 6.0 years ago by 21k • written 6.0 years ago by • 0
0
votes
6
replies
2.0k
views
Opening Illumina HT12 V3.0 Data from GEO
limma normalization GEO
6.1 years ago FL512 • 0
3
votes
2
replies
1.6k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart geo software error ensembl
updated 6.4 years ago by ★ 6.6k • written 6.4 years ago by ▴ 10
0
votes
0
replies
1.4k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
3
votes
6
replies
4.3k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
6.5 years ago andy_shaps ▴ 10
5
votes
12
replies
3.6k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 7.2 years ago by 21k • written 7.2 years ago by ▴ 20
1
vote
3
replies
1.3k
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 20
2
votes
6
replies
2.4k
views
error reading GSE using getGEO()
r geo getgeo
7.3 years ago jaleh.amo • 0
3
votes
2
replies
1.9k
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb GEO R bioconductor
updated 7.3 years ago by 21k • written 7.3 years ago by ▴ 20
1
vote
2
replies
2.2k
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 7.4 years ago by 68k • written 7.4 years ago by • 0
0
votes
4
replies
2.1k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 7.4 years ago by 21k • written 7.4 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
7.4 years ago daniel.green • 0
1
vote
1
reply
1.8k
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 10
3
votes
11
replies
5.4k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 7.8 years ago by 21k • written 8.6 years ago by • 0
3
votes
5
replies
6.6k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
7.8 years ago martinguerrerog89 ▴ 20
10
votes
7
replies
3.3k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 7.9 years ago by 21k • written 7.9 years ago by ▴ 60
1
vote
3
replies
3.0k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
0
votes
1
reply
2.0k
views
GEOquery download error
geoquery error message GEOquery GSE GEO
8.2 years ago Barah ▴ 20
1
vote
3
replies
2.0k
views
Getting gene annotation for a GEO dataset
geo
8.3 years ago yuvallb • 0
2
votes
2
replies
3.0k
views
GEOquery error in downloading SOFT files
geoquery getgeo GEO
9.0 years ago hzc363 ▴ 20
0
votes
1
reply
2.7k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 30
2
votes
4
replies
2.1k
views
read bead-level data directly by lumi
bead-level GEO lumi
updated 9.7 years ago by ★ 6.6k • written 9.7 years ago by • 0
1
vote
2
replies
1.8k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray bead-level GEO lumi
updated 9.7 years ago by ★ 6.6k • written 9.7 years ago by • 0
0
votes
1
reply
1.4k
views
data handling from GSE22216 to exprSet object
GEO
updated 9.8 years ago by ★ 6.6k • written 9.8 years ago by ▴ 10
0
votes
5
replies
2.5k
views
collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 10.0 years ago by ★ 3.4k • written 10.0 years ago by • 0
0
votes
1
reply
1.6k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
51 results • Page 1 of 2
Recent ...
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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