Showing : geoquery • reset
0
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4
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416
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 8 weeks ago by 21k • written 8 weeks ago by • 0
0
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9
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581
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
11 weeks ago • updated 10 weeks ago gallantk5 • 0
1
vote
5
replies
627
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 3 months ago by ★ 4.4k • written 3 months ago by • 0
0
votes
3
replies
437
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 4 months ago by 67k • written 4 months ago by • 0
0
votes
7
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862
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
5 months ago needNGS • 0
0
votes
1
reply
633
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
13 months ago Arianna • 0
0
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2
replies
862
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 17 months ago by 51k • written 17 months ago by • 0
0
votes
2
replies
727
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 17 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
779
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 19 months ago by 67k • written 19 months ago by • 0
0
votes
1
reply
634
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
3
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2
replies
1.6k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.1 years ago by 4.0k • written 2.1 years ago by ▴ 10
0
votes
1
reply
753
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
vote
5
replies
1.3k
views
Can't read in CEL files
GEO GEOquery
2.2 years ago OE • 0
0
votes
2
replies
1.2k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.3 years ago Yugang • 0
2
votes
1
reply
2.8k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.5 years ago by ▴ 100 • written 2.5 years ago by • 0
5
votes
7
replies
2.5k
views
GEO series matrix empty
GEOquery GEO
2.6 years ago • updated 2.5 years ago gs.123 ▴ 20
3
votes
2
replies
1.4k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.7 years ago by 21k • written 2.7 years ago by ▴ 30
3
votes
23
replies
4.3k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
2.8 years ago array chip ▴ 420
1
vote
2
replies
2.7k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 10
0
votes
1
reply
2.4k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
2
votes
3
replies
1.5k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 2.8 years ago by ★ 13k • written 2.8 years ago by ▴ 50
6
votes
7
replies
2.5k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 2.8 years ago by 67k • written 2.8 years ago by ▴ 50
1
vote
1
reply
1.3k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.0 years ago by 67k • written 3.0 years ago by ▴ 50
1
vote
1
reply
1.7k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 10
0
votes
1
reply
952
views
GEOquery
GEOquery
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by ▴ 10
6
votes
5
replies
1.4k
views
a problem of package ""
GEO GEOquery
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 20
2
votes
3
replies
1.2k
views
Problem about Geoquery
GEO GEOquery
3.3 years ago sheldon19931016 ▴ 20
7
votes
5
replies
6.5k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.3 years ago by 21k
0
votes
5
replies
3.8k
views
assayData: 0 features
geoquery
updated 3.5 years ago by ▴ 10 • written 9.0 years ago by ▴ 230
3
votes
4
replies
1.5k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 20
3
votes
1
reply
1.1k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 3.7 years ago by 51k • written 3.7 years ago by • 0
0
votes
2
replies
2.1k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 3.9 years ago by 1.6k • written 3.9 years ago by • 0
6
votes
3
replies
1.6k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 40
1
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1
reply
1.2k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.4 years ago by ★ 3.4k • written 4.4 years ago by • 0
5
votes
5
replies
1.4k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 830
0
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1
reply
1.1k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.7 years ago by ★ 13k • written 4.7 years ago by • 0
0
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3
replies
1.2k
views
GEOquery and Feature data
GEOquery featureNames
updated 4.8 years ago by 21k • written 4.8 years ago by • 0
0
votes
3
replies
1.9k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 4.9 years ago by 67k • written 4.9 years ago by ▴ 20
3
votes
2
replies
2.5k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 4.9 years ago by 67k • written 4.9 years ago by ▴ 20
2
votes
1
reply
1.5k
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.9 years ago by 21k • written 4.9 years ago by ▴ 730
0
votes
5
replies
2.3k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.2 years ago by 67k • written 5.2 years ago by • 0
0
votes
0
replies
1.1k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.3 years ago by 67k • written 5.3 years ago by ▴ 10
3
votes
6
replies
3.3k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.4 years ago andy_shaps ▴ 10
1
vote
2
replies
1.4k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.4 years ago by 67k • written 5.4 years ago by • 0
3
votes
4
replies
1.7k
views
GEOquery:Get error sampleNames
geoquery
updated 5.7 years ago by 0 • written 5.8 years ago by ▴ 10
2
votes
2
replies
2.2k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.3k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
5.8 years ago cschot3 • 0
0
votes
0
replies
1.1k
views
Query based on PMIDs
SRAdb geoquery
5.8 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
2.8k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 20
2
votes
3
replies
1.8k
views
Filtering the probe set ids from GSE file
geoquery GSE
6.0 years ago mahm ▴ 20
50 results • Page 1 of 1
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Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
I request the post here, so not a problem.
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by micolak0115 • 0
Thanks for the advice Michael. I will try this with my future test datasets.
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by micolak0115 • 0
Hi James, I will try to leave only relevant questions on bioconductor forum hereinafter. Thanks for the note. Cheers, Alan
Comment: SingleR Label.Ont by Stepah • 0
[Aussie Play][1] cares about its Australian players by offering a safe and secure gaming experience where there is never a dull moment. The…
Comment: ensemblVEP deprecation and how to reproduce by Vincent J. Carey, Jr. 6.7k
What aspect of ensemblVEP are you looking for? The vignette https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/in…
Votes
DEXseq: How to do differential exon usage of genes with overlapping exons
A: Moderated F-test followed by moderated t-test in limma
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
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