Showing : GEOquery • reset
2
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4
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313
views
Converting Probe IDs to HGNC symbols
Annotation biomaRt GEOquery
written 6 weeks ago by ▴ 10
0
votes
1
reply
411
views
best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 10 months ago by 68k • written 10 months ago by • 0
1
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2
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570
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 15 months ago by 68k • written 15 months ago by • 0
0
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4
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1.7k
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 19 months ago by 21k • written 19 months ago by • 0
0
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9
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1.6k
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
20 months ago • updated 19 months ago gallantk5 • 0
1
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5
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3.8k
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Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
votes
3
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1.1k
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
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7
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2.5k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
22 months ago needNGS • 0
0
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1
reply
1.4k
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.6 years ago Arianna • 0
0
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2
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1.4k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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2
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1.2k
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
0
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1
reply
1.2k
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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1
reply
1.1k
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
3
votes
2
replies
2.5k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 3.5 years ago by 4.3k • written 3.5 years ago by ▴ 10
0
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1
reply
1.1k
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
1
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5
replies
2.2k
views
Can't read in CEL files
GEO GEOquery
3.7 years ago OE • 0
0
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2
replies
1.9k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
3.8 years ago Yugang • 0
2
votes
1
reply
5.2k
views
Error in downloading GEO Supplementary files
GEOquery
updated 3.9 years ago by ▴ 100 • written 3.9 years ago by • 0
5
votes
7
replies
4.0k
views
GEO series matrix empty
GEOquery GEO
4.0 years ago gs.123 ▴ 20
3
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2
replies
1.9k
views
GEOquery returning NAs as probe names
GEOquery
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 30
3
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23
replies
6.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
4.2 years ago array chip ▴ 420
1
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2
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4.1k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
0
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1
reply
3.0k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 4.2 years ago by ▴ 780 • written 4.2 years ago by • 0
2
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3
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2.4k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 4.2 years ago by ★ 13k • written 4.3 years ago by ▴ 50
6
votes
7
replies
3.7k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 50
1
vote
1
reply
1.9k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 50
1
vote
1
reply
2.5k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 10
0
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1
reply
1.4k
views
GEOquery
GEOquery
updated 4.7 years ago by ▴ 780 • written 4.7 years ago by ▴ 10
6
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5
replies
2.0k
views
a problem of package ""
GEO GEOquery
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 20
2
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3
replies
1.9k
views
Problem about Geoquery
GEO GEOquery
4.7 years ago sheldon19931016 ▴ 20
7
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5
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7.5k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 10.7 years ago by 21k
0
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5
replies
4.8k
views
assayData: 0 features
geoquery
updated 5.0 years ago by ▴ 10 • written 10.4 years ago by ▴ 230
3
votes
4
replies
2.1k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 5.1 years ago by 21k • written 5.1 years ago by ▴ 20
3
votes
1
reply
1.6k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
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2
replies
3.3k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 5.3 years ago by 1.6k • written 5.3 years ago by • 0
6
votes
3
replies
2.3k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 5.7 years ago by 21k • written 5.7 years ago by ▴ 40
1
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1
reply
1.9k
views
Table expression data from GEO file
GEO expression GEOquery
updated 5.8 years ago by ★ 3.4k • written 5.8 years ago by • 0
5
votes
5
replies
2.0k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 840
0
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1
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1.6k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 6.1 years ago by ★ 13k • written 6.1 years ago by • 0
0
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3
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1.7k
views
GEOquery and Feature data
GEOquery featureNames
updated 6.3 years ago by 21k • written 6.3 years ago by • 0
0
votes
3
replies
2.5k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 20
3
votes
2
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3.2k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 20
2
votes
1
reply
2.5k
views
Downloading a private GEO with GEOquery
GEOquery
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 760
0
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5
replies
3.1k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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0
replies
1.4k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 10
3
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6
replies
4.5k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
6.8 years ago andy_shaps ▴ 10
1
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2
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2.0k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
3
votes
4
replies
2.1k
views
GEOquery:Get error sampleNames
geoquery
updated 7.1 years ago by 0 • written 7.2 years ago by ▴ 10
2
votes
2
replies
2.7k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 10
0
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2
replies
1.8k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
7.2 years ago cschot3 • 0
242 results • Page 1 of 5
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Replies
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to Peter Hickey &utrif; 760
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