Showing : GEOquery • reset
1
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 29 days ago by 67k • written 29 days ago by • 0
0
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4
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656
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 5 months ago by 21k • written 5 months ago by • 0
0
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9
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760
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
5 months ago gallantk5 • 0
1
vote
5
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1.4k
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
0
votes
3
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544
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
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7
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1.2k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
8 months ago needNGS • 0
0
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1
reply
750
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
17 months ago Arianna • 0
0
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2
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966
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 20 months ago by 52k • written 20 months ago by • 0
0
votes
2
replies
798
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 21 months ago by • 0 • written 21 months ago by • 0
0
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1
reply
848
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 22 months ago by 67k • written 22 months ago by • 0
0
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1
reply
711
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
3
votes
2
replies
1.8k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.3 years ago by 4.1k • written 2.3 years ago by ▴ 10
0
votes
1
reply
815
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
1
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5
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1.4k
views
Can't read in CEL files
GEO GEOquery
2.5 years ago OE • 0
0
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2
replies
1.3k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.6 years ago Yugang • 0
2
votes
1
reply
3.2k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.7 years ago by ▴ 100 • written 2.7 years ago by • 0
5
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7
replies
2.6k
views
GEO series matrix empty
GEOquery GEO
2.8 years ago gs.123 ▴ 20
3
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2
replies
1.5k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.9 years ago by 21k • written 2.9 years ago by ▴ 30
3
votes
23
replies
4.6k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.0 years ago array chip ▴ 420
1
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2
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2.9k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.0 years ago by 21k • written 3.1 years ago by ▴ 10
0
votes
1
reply
2.5k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
2
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3
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1.6k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.1 years ago by ★ 13k • written 3.1 years ago by ▴ 50
6
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7
replies
2.7k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 50
1
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1
reply
1.4k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.3 years ago by 67k • written 3.3 years ago by ▴ 50
1
vote
1
reply
1.9k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
GEOquery
GEOquery
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by ▴ 10
6
votes
5
replies
1.5k
views
a problem of package ""
GEO GEOquery
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 20
2
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3
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1.3k
views
Problem about Geoquery
GEO GEOquery
3.6 years ago sheldon19931016 ▴ 20
7
votes
5
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6.7k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.5 years ago by 21k
0
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5
replies
4.0k
views
assayData: 0 features
geoquery
updated 3.8 years ago by ▴ 10 • written 9.3 years ago by ▴ 230
3
votes
4
replies
1.6k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 20
3
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1
reply
1.2k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 4.0 years ago by 52k • written 4.0 years ago by • 0
0
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2
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2.5k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 4.2 years ago by 1.6k • written 4.2 years ago by • 0
6
votes
3
replies
1.7k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 40
1
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1
reply
1.3k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by • 0
5
votes
5
replies
1.5k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 840
0
votes
1
reply
1.2k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
0
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3
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1.3k
views
GEOquery and Feature data
GEOquery featureNames
updated 5.1 years ago by 21k • written 5.1 years ago by • 0
0
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3
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2.0k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 5.1 years ago by 67k • written 5.1 years ago by ▴ 20
3
votes
2
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2.7k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 20
2
votes
1
reply
1.6k
views
Downloading a private GEO with GEOquery
GEOquery
updated 5.2 years ago by 21k • written 5.2 years ago by ▴ 760
0
votes
5
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2.4k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.4 years ago by 67k • written 5.4 years ago by • 0
0
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0
replies
1.1k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 10
3
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6
replies
3.5k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.6 years ago andy_shaps ▴ 10
1
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2
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1.5k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
3
votes
4
replies
1.7k
views
GEOquery:Get error sampleNames
geoquery
updated 5.9 years ago by 0 • written 6.1 years ago by ▴ 10
2
votes
2
replies
2.3k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.0 years ago by 67k • written 6.0 years ago by ▴ 10
0
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2
replies
1.4k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.1 years ago cschot3 • 0
0
votes
0
replies
1.1k
views
Query based on PMIDs
SRAdb geoquery
6.1 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
3.0k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k
I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
Awards • All
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Popular Question to Benjamin ▴ 20
Popular Question to María Calvo • 0
Popular Question to Gordon Smyth 52k
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