Showing : GEOquery • reset
0
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2
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71
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How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
4 days ago • updated 3 days ago Yugang • 0
0
votes
1
reply
105
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Error in downloading GEO Supplementary files
GEOquery
updated 8 weeks ago by ▴ 70 • written 8 weeks ago by • 0
5
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7
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383
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GEO series matrix empty
GEOquery GEO
12 weeks ago • updated 10 weeks ago gs.123 ▴ 20
3
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2
replies
286
views
GEOquery returning NAs as probe names
GEOquery
updated 4 months ago by 21k • written 4 months ago by ▴ 30
3
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23
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1.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
5 months ago array chip ▴ 420
1
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2
replies
439
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 5 months ago by 21k • written 5 months ago by ▴ 10
0
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1
reply
471
views
Data frame with 0 columns and 0 rows
GEOquery
updated 5 months ago by ▴ 280 • written 5 months ago by • 0
2
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3
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309
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 6 months ago by 13k • written 6 months ago by ▴ 50
6
votes
7
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664
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 6 months ago by 59k • written 6 months ago by ▴ 50
1
vote
1
reply
433
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 8 months ago by 59k • written 8 months ago by ▴ 50
1
vote
1
reply
224
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 10 months ago by 21k • written 10 months ago by ▴ 10
0
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1
reply
295
views
GEOquery
GEOquery
updated 11 months ago by ▴ 280 • written 11 months ago by • 0
6
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5
replies
440
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a problem of package ""
GEO GEOquery
updated 11 months ago by 15k • written 11 months ago by ▴ 20
2
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3
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294
views
Problem about Geoquery
GEO GEOquery
11 months ago sheldon19931016 ▴ 20
7
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3
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4.0k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
7.0 years ago • updated 10 months ago Sean Davis 21k
0
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5
replies
1.7k
views
assayData: 0 features
geoquery
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 230
3
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4
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553
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 15 months ago by 21k • written 15 months ago by ▴ 20
3
votes
1
reply
318
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 17 months ago by 45k • written 17 months ago by • 0
0
votes
2
replies
571
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 19 months ago by 1.5k • written 19 months ago by • 0
6
votes
3
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530
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 23 months ago by 21k • written 23 months ago by ▴ 40
1
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1
reply
308
views
Table expression data from GEO file
GEO expression GEOquery
updated 2.1 years ago by ★ 2.8k • written 2.1 years ago by • 0
4
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5
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485
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Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 2.1 years ago by 59k • written 2.1 years ago by ▴ 780
0
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1
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417
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 2.3 years ago by 13k • written 2.3 years ago by • 0
0
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3
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355
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GEOquery and Feature data
GEOquery featureNames
updated 2.5 years ago by 21k • written 2.5 years ago by • 0
0
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3
replies
786
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 2.6 years ago by 59k • written 2.6 years ago by ▴ 20
2
votes
2
replies
983
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 2.6 years ago by 59k • written 2.6 years ago by ▴ 20
2
votes
1
reply
474
views
Downloading a private GEO with GEOquery
GEOquery
updated 2.6 years ago by 21k • written 2.6 years ago by ▴ 660
0
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5
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1.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 2.9 years ago by 59k • written 2.9 years ago by • 0
0
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0
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414
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 3.0 years ago by 59k • written 3.0 years ago by ▴ 10
3
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6
replies
1.6k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
3.0 years ago andy_shaps ▴ 10
1
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2
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569
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 3.1 years ago by 59k • written 3.1 years ago by • 0
3
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4
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881
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GEOquery:Get error sampleNames
geoquery
updated 3.3 years ago by 0 • written 3.5 years ago by ▴ 10
2
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2
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1.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 3.4 years ago by 59k • written 3.4 years ago by ▴ 10
0
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2
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628
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
3.5 years ago cschot3 • 0
0
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0
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485
views
Query based on PMIDs
SRAdb geoquery
3.5 years ago Deepak Tanwar ▴ 10
5
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12
replies
1.4k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 20
2
votes
3
replies
782
views
Filtering the probe set ids from GSE file
geoquery GSE
3.7 years ago mahm ▴ 20
3
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11
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1.2k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 20
3
votes
2
replies
903
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 10
0
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1
reply
807
views
question about getGEO function
geoquery
3.8 years ago maryam.sabet • 0
0
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1
reply
469
views
GEOquery install problem
geoquery
3.8 years ago 261092095 ▴ 10
3
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5
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1.3k
views
getGEO function doesn't download the expression data
geoquery
updated 3.8 years ago by ▴ 990 • written 3.8 years ago by ▴ 10
0
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4
replies
713
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 10
1
vote
4
replies
1.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 10
1
vote
2
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689
views
Error when Creating Expression Set from Geo Set
geoquery
4.1 years ago dmm204 • 0
2
votes
2
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743
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 4.1 years ago by 59k • written 4.1 years ago by • 0
3
votes
2
replies
1.8k
views
getGEO error when trying to download a series matrix file
GEOquery getGEO
4.2 years ago rubi ▴ 100
2
votes
3
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688
views
GEO2R Gene Expression
geoquery
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
1
vote
1
reply
646
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
3
votes
4
replies
839
views
getGEO Error: Duplicate identifiers for rows
geoquery getgeo
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by Yang Shi • 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available by swbarnes2 ★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by James W. MacDonald 59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o by Yang Shi • 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Use MulticoreParam under BatchtoolsParam
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
Awards • All
Popular Question to Johannes Rainer ★ 1.9k
Popular Question to Gordon Smyth 45k
Popular Question to Julie Zhu ★ 4.3k
Scholar to Hervé Pagès 15k
Commentator to James W. MacDonald 59k
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