Showing : GEOquery • reset
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best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
1
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2
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366
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 5 months ago by 68k • written 5 months ago by • 0
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4
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1.0k
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 9 months ago by 21k • written 9 months ago by • 0
0
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9
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999
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
10 months ago • updated 9 months ago gallantk5 • 0
1
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5
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2.5k
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Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 10 months ago by ★ 4.8k • written 10 months ago by • 0
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3
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695
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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 11 months ago by 68k • written 11 months ago by • 0
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7
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1.8k
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
12 months ago needNGS • 0
0
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1
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879
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
21 months ago Arianna • 0
0
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2
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1.1k
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
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2
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902
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
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1
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947
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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1
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824
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
3
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2
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2.1k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.7 years ago by 4.1k • written 2.7 years ago by ▴ 10
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1
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894
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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5
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1.7k
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Can't read in CEL files
GEO GEOquery
2.9 years ago OE • 0
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2
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1.5k
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How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
3.0 years ago • updated 2.9 years ago Yugang • 0
2
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1
reply
3.9k
views
Error in downloading GEO Supplementary files
GEOquery
updated 3.1 years ago by ▴ 100 • written 3.1 years ago by • 0
5
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7
replies
3.0k
views
GEO series matrix empty
GEOquery GEO
3.2 years ago • updated 3.1 years ago gs.123 ▴ 20
3
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2
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1.6k
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GEOquery returning NAs as probe names
GEOquery
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 30
3
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23
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5.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.4 years ago array chip ▴ 420
1
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2
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3.2k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
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1
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2.7k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
2
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3
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1.9k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.4 years ago by ★ 13k • written 3.4 years ago by ▴ 50
6
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7
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3.1k
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GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 50
1
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1
reply
1.6k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 50
1
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1
reply
2.1k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 3.8 years ago by 21k • written 3.8 years ago by ▴ 10
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1
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1.1k
views
GEOquery
GEOquery
updated 3.9 years ago by ▴ 780 • written 3.9 years ago by ▴ 10
6
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5
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1.7k
views
a problem of package ""
GEO GEOquery
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 20
2
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3
replies
1.5k
views
Problem about Geoquery
GEO GEOquery
3.9 years ago sheldon19931016 ▴ 20
7
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5
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6.9k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.9 years ago by 21k
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5
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4.3k
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assayData: 0 features
geoquery
updated 4.2 years ago by ▴ 10 • written 9.6 years ago by ▴ 230
3
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4
replies
1.8k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 20
3
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1
reply
1.3k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
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2
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2.8k
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Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 4.5 years ago by 1.6k • written 4.5 years ago by • 0
6
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3
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1.8k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.9 years ago by 21k • written 4.9 years ago by ▴ 40
1
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1
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1.5k
views
Table expression data from GEO file
GEO expression GEOquery
updated 5.0 years ago by ★ 3.4k • written 5.0 years ago by • 0
5
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5
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1.6k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 840
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1
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1.3k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 5.3 years ago by ★ 13k • written 5.3 years ago by • 0
0
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3
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1.5k
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GEOquery and Feature data
GEOquery featureNames
updated 5.4 years ago by 21k • written 5.4 years ago by • 0
0
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3
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2.1k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
3
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2
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2.9k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
2
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1
reply
1.9k
views
Downloading a private GEO with GEOquery
GEOquery
updated 5.5 years ago by 21k • written 5.5 years ago by ▴ 760
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5
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2.6k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
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0
replies
1.2k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
3
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6
replies
4.0k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
6.0 years ago andy_shaps ▴ 10
1
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2
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1.7k
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How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
3
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4
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1.9k
views
GEOquery:Get error sampleNames
geoquery
updated 6.3 years ago by 0 • written 6.4 years ago by ▴ 10
2
votes
2
replies
2.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 10
0
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2
replies
1.5k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.4 years ago cschot3 • 0
0
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0
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1.2k
views
Query based on PMIDs
SRAdb geoquery
6.4 years ago Deepak Tanwar ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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Scholar to Gordon Smyth 52k
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