Showing : GEOquery • reset
1
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66
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unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 17 days ago by 21k • written 17 days ago by ▴ 10
0
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1
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112
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GEOquery
GEOquery
updated 8 weeks ago by ▴ 150 • written 9 weeks ago by • 0
6
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5
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181
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a problem of package ""
GEO GEOquery
updated 9 weeks ago by 15k • written 9 weeks ago by ▴ 20
2
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3
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116
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Problem about Geoquery
GEO GEOquery
9 weeks ago sheldon19931016 ▴ 20
7
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3
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3.2k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
6.2 years ago • updated 17 days ago Sean Davis 21k
0
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5
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1.4k
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assayData: 0 features
geoquery
updated 5 months ago by • 0 • written 5.9 years ago by ▴ 230
3
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4
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298
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when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 6 months ago by 21k • written 6 months ago by ▴ 20
3
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1
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179
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Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 7 months ago by 43k • written 7 months ago by • 0
0
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2
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317
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Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 9 months ago by 1.5k • written 9 months ago by • 0
6
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3
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261
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GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 13 months ago by 21k • written 13 months ago by ▴ 40
1
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1
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153
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Table expression data from GEO file
GEO expression GEOquery
updated 15 months ago by ★ 2.7k • written 15 months ago by • 0
4
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5
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251
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Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 16 months ago by 57k • written 16 months ago by ▴ 780
0
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1
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215
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I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 18 months ago by 13k • written 18 months ago by • 0
0
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3
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211
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GEOquery and Feature data
GEOquery featureNames
updated 20 months ago by 21k • written 20 months ago by • 0
0
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3
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476
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When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 21 months ago by 57k • written 21 months ago by • 0
2
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2
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552
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 21 months ago by 57k • written 21 months ago by • 0
2
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1
reply
244
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Downloading a private GEO with GEOquery
GEOquery
updated 22 months ago by 21k • written 22 months ago by ▴ 650
0
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5
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747
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Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.1 years ago by 57k • written 2.1 years ago by • 0
0
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0
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296
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GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 2.2 years ago by 57k • written 2.2 years ago by ▴ 10
3
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6
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1.0k
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GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
2.3 years ago andy_shaps ▴ 10
1
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2
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400
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How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 2.3 years ago by 57k • written 2.3 years ago by • 0
3
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4
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660
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GEOquery:Get error sampleNames
geoquery
updated 2.6 years ago by 0 • written 2.7 years ago by ▴ 10
2
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2
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1.2k
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geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 2.6 years ago by 57k • written 2.6 years ago by ▴ 10
0
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2
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446
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GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
2.7 years ago cschot3 • 0
0
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0
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354
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Query based on PMIDs
SRAdb geoquery
2.7 years ago Deepak Tanwar ▴ 10
5
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12
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845
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Using eset while parsing GSE file located in a path
GEO geoquery
updated 2.9 years ago by 21k • written 2.9 years ago by ▴ 20
2
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3
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549
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Filtering the probe set ids from GSE file
geoquery GSE
2.9 years ago mahm ▴ 20
3
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11
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871
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Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 2.9 years ago by 21k • written 2.9 years ago by ▴ 20
3
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2
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622
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 10
0
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1
reply
588
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question about getGEO function
geoquery
3.0 years ago maryam.sabet • 0
0
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1
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379
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GEOquery install problem
geoquery
3.0 years ago 261092095 ▴ 10
3
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5
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934
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getGEO function doesn't download the expression data
geoquery
updated 3.1 years ago by ▴ 980 • written 3.1 years ago by ▴ 10
0
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4
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512
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GEOquery using keywords in R
GEO geoquery geometadb
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 10
1
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4
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740
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Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 10
1
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2
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562
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Error when Creating Expression Set from Geo Set
geoquery
3.3 years ago dmm204 • 0
2
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2
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577
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getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 3.4 years ago by 57k • written 3.4 years ago by • 0
3
votes
2
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1.3k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
3.4 years ago rubi ▴ 90
2
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3
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473
views
GEO2R Gene Expression
geoquery
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
1
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1
reply
470
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
3
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4
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664
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getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
1
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7
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643
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model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
3.4 years ago darthratus • 0
3
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11
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1.9k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 3.5 years ago by 21k • written 4.3 years ago by • 0
0
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1
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903
views
GEOquery getGEO 404
geoquery geoquery error message
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 20
3
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5
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2.0k
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Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
3.5 years ago martinguerrerog89 ▴ 20
10
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7
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1.1k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 60
1
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3
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634
views
Boxplot and Identification of DEG
limma biobase geoquery
updated 3.7 years ago by ★ 27k • written 3.7 years ago by ▴ 20
3
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3
replies
634
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How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
geoquery summarizedexperiment rangedsummarizedexperiment
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 100
1
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3
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1.2k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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1
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716
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GEOquery download error
geoquery error message GEOquery GSE GEO
3.9 years ago Barah ▴ 20
3
votes
3
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2.2k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
Comment: P value and Adj. P value showing N/A
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