Showing : Geoquery • reset
1
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 3 months ago by 68k • written 3 months ago by • 0
0
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4
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877
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 7 months ago by 21k • written 7 months ago by • 0
0
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9
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913
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
8 months ago gallantk5 • 0
1
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5
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2.1k
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 9 months ago by ★ 4.7k • written 9 months ago by • 0
0
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3
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640
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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 10 months ago by 68k • written 10 months ago by • 0
0
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7
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1.5k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
11 months ago needNGS • 0
0
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1
reply
838
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
19 months ago Arianna • 0
0
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2
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1.0k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 23 months ago by 52k • written 23 months ago by • 0
0
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2
replies
865
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 23 months ago by • 0 • written 23 months ago by • 0
0
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1
reply
912
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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1
reply
788
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empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
3
votes
2
replies
2.0k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.6 years ago by 4.1k • written 2.6 years ago by ▴ 10
0
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1
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873
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Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
1
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5
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1.6k
views
Can't read in CEL files
GEO GEOquery
2.7 years ago OE • 0
0
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2
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1.4k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.8 years ago Yugang • 0
2
votes
1
reply
3.6k
views
Error in downloading GEO Supplementary files
GEOquery
updated 3.0 years ago by ▴ 100 • written 3.0 years ago by • 0
5
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7
replies
2.9k
views
GEO series matrix empty
GEOquery GEO
3.0 years ago gs.123 ▴ 20
3
votes
2
replies
1.6k
views
GEOquery returning NAs as probe names
GEOquery
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 30
3
votes
23
replies
4.9k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.3 years ago array chip ▴ 420
1
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2
replies
3.1k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 10
0
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1
reply
2.7k
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Data frame with 0 columns and 0 rows
GEOquery
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
2
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3
replies
1.8k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.3 years ago by ★ 13k • written 3.3 years ago by ▴ 50
6
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7
replies
2.9k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 50
1
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1
reply
1.5k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 50
1
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1
reply
2.0k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.1k
views
GEOquery
GEOquery
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by ▴ 10
6
votes
5
replies
1.6k
views
a problem of package ""
GEO GEOquery
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 20
2
votes
3
replies
1.4k
views
Problem about Geoquery
GEO GEOquery
3.8 years ago sheldon19931016 ▴ 20
7
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5
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6.8k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.8 years ago by 21k
0
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5
replies
4.2k
views
assayData: 0 features
geoquery
updated 4.0 years ago by ▴ 10 • written 9.5 years ago by ▴ 230
3
votes
4
replies
1.8k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 20
3
votes
1
reply
1.3k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 4.2 years ago by 52k • written 4.2 years ago by • 0
0
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2
replies
2.7k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 4.4 years ago by 1.6k • written 4.4 years ago by • 0
6
votes
3
replies
1.8k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.7 years ago by 21k • written 4.7 years ago by ▴ 40
1
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1
reply
1.4k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.9 years ago by ★ 3.4k • written 4.9 years ago by • 0
5
votes
5
replies
1.6k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 840
0
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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 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
0
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3
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1.4k
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GEOquery and Feature data
GEOquery featureNames
updated 5.3 years ago by 21k • written 5.3 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 5.4 years ago by 68k • written 5.4 years ago by ▴ 20
3
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2
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2.8k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 20
2
votes
1
reply
1.8k
views
Downloading a private GEO with GEOquery
GEOquery
updated 5.4 years ago by 21k • written 5.4 years ago by ▴ 760
0
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5
replies
2.5k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
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0
replies
1.2k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 10
3
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6
replies
3.8k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.9 years ago andy_shaps ▴ 10
1
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2
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1.6k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
3
votes
4
replies
1.8k
views
GEOquery:Get error sampleNames
geoquery
updated 6.2 years ago by 0 • written 6.3 years ago by ▴ 10
2
votes
2
replies
2.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 10
0
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2
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1.5k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.3 years ago cschot3 • 0
0
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0
replies
1.2k
views
Query based on PMIDs
SRAdb geoquery
6.3 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
3.1k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.5 years ago by 21k • written 6.5 years ago by ▴ 20
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Answer: library org.Hs.eg.db failing to install by James W. MacDonald 68k
It should just install. ``` > library(BiocManager) Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14 ucrt) W…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Thank you so much for your quick reply! I was worried if some underlying technical artifact or unusual behavior would be causing the patter…
Answer: Surprising behavior for DEXseq dispersion estimate plot? by Michael Love 43k
The red points are just slowly moving toward -Inf. They tend to have variance < mean (if it were a simple design and you could just look at…
Answer: DESeq use in lipidomic analysis by Michael Love 43k
I would go for limma rather than a NB-based method. See the papers on limma for metabolomics / proteomics.
Answer: DiffBind - question on the use of filtered or unfiltered input data by robert • 0
[FFH4X][1] Injector is a Free Fire mod menu software that includes a variety of intriguing hack features such as aimbot, auto headshot, fly…
Votes
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Calculating TOM in blockwise WGCNA
A: What is the "linear model" part used for in Limma?
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