Showing : Geoquery • reset
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
19 days ago • updated 16 days ago needNGS • 0
0
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1
reply
452
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
0
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2
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664
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
2
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559
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 12 months ago by • 0 • written 13 months ago by • 0
0
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1
reply
611
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
0
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1
reply
482
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 17 months ago by ▴ 770 • written 17 months ago by • 0
3
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2
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1.3k
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Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 20 months ago by 3.8k • written 20 months ago by ▴ 10
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1
reply
634
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Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 21 months ago by ▴ 770 • written 21 months ago by • 0
1
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5
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1.0k
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Can't read in CEL files
GEO GEOquery
22 months ago OE • 0
0
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2
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948
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How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
23 months ago Yugang • 0
1
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1
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2.4k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by • 0
5
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7
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2.1k
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GEO series matrix empty
GEOquery GEO
2.2 years ago • updated 2.1 years ago gs.123 ▴ 20
3
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2
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1.2k
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GEOquery returning NAs as probe names
GEOquery
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 30
3
votes
23
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3.8k
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GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
2.4 years ago array chip ▴ 420
1
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2
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2.3k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 10
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1
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2.1k
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Data frame with 0 columns and 0 rows
GEOquery
updated 2.4 years ago by ▴ 770 • written 2.4 years ago by • 0
2
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3
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1.2k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 2.4 years ago by ★ 13k • written 2.4 years ago by ▴ 50
6
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7
replies
2.1k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 2.4 years ago by 65k • written 2.4 years ago by ▴ 50
1
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1
reply
1.1k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.6 years ago by 65k • written 2.6 years ago by ▴ 50
1
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1
reply
1.4k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 10
0
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1
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847
views
GEOquery
GEOquery
updated 2.9 years ago by ▴ 770 • written 2.9 years ago by ▴ 10
6
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5
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1.2k
views
a problem of package ""
GEO GEOquery
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 20
2
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3
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971
views
Problem about Geoquery
GEO GEOquery
2.9 years ago sheldon19931016 ▴ 20
7
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5
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6.0k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.9 years ago by 21k
0
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5
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3.4k
views
assayData: 0 features
geoquery
updated 3.1 years ago by ▴ 10 • written 8.6 years ago by ▴ 230
3
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4
replies
1.3k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 20
3
votes
1
reply
932
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 3.3 years ago by 50k • written 3.3 years ago by • 0
0
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2
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1.8k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 3.5 years ago by 1.6k • written 3.5 years ago by • 0
6
votes
3
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1.3k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 40
1
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1
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1.1k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by • 0
5
votes
5
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1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
0
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1
reply
986
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.3 years ago by ★ 13k • written 4.3 years ago by • 0
0
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3
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1.0k
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GEOquery and Feature data
GEOquery featureNames
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
votes
3
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1.7k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
3
votes
2
replies
2.2k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 20
2
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1
reply
1.3k
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 730
0
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5
replies
2.0k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
0
votes
0
replies
939
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
3
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6
replies
2.9k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.0 years ago andy_shaps ▴ 10
1
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2
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1.3k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.3 years ago by 0 • written 5.4 years ago by ▴ 10
2
votes
2
replies
2.0k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.3 years ago by 65k • written 5.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.4 years ago cschot3 • 0
0
votes
0
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930
views
Query based on PMIDs
SRAdb geoquery
5.4 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
2.6k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 5.6 years ago by 21k • written 5.6 years ago by ▴ 20
2
votes
3
replies
1.6k
views
Filtering the probe set ids from GSE file
geoquery GSE
5.6 years ago mahm ▴ 20
3
votes
11
replies
2.3k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.6 years ago by 21k • written 5.6 years ago by ▴ 20
3
votes
2
replies
1.7k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
question about getGEO function
geoquery
5.7 years ago maryam.sabet • 0
0
votes
1
reply
867
views
GEOquery install problem
geoquery
5.7 years ago 261092095 ▴ 10
50 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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