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 7 months ago by 68k • written 7 months ago by • 0
1
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2
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502
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 11 months ago by 68k • written 11 months ago by • 0
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4
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1.4k
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Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 15 months ago by 21k • written 15 months ago by • 0
0
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9
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1.3k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
16 months ago gallantk5 • 0
1
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5
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3.0k
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Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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3
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883
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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7
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2.2k
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
19 months ago needNGS • 0
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1
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1.1k
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.3 years ago Arianna • 0
0
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2
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1.2k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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2
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1.1k
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
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1
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1.1k
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
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1
reply
959
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
3
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2
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2.3k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 3.2 years ago by 4.2k • written 3.2 years ago by ▴ 10
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1
reply
1.0k
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
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5
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2.0k
views
Can't read in CEL files
GEO GEOquery
3.4 years ago OE • 0
0
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2
replies
1.7k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
3.5 years ago Yugang • 0
2
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1
reply
4.5k
views
Error in downloading GEO Supplementary files
GEOquery
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by • 0
5
votes
7
replies
3.4k
views
GEO series matrix empty
GEOquery GEO
3.7 years ago gs.123 ▴ 20
3
votes
2
replies
1.7k
views
GEOquery returning NAs as probe names
GEOquery
updated 3.8 years ago by 21k • written 3.8 years ago by ▴ 30
3
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23
replies
5.6k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.9 years ago array chip ▴ 420
1
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2
replies
3.6k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
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1
reply
2.9k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
2
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3
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2.1k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 4.0 years ago by ★ 13k • written 4.0 years ago by ▴ 50
6
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7
replies
3.4k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 50
1
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1
reply
1.7k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 50
1
vote
1
reply
2.3k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 4.3 years ago by 21k • written 4.3 years ago by ▴ 10
0
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1
reply
1.3k
views
GEOquery
GEOquery
updated 4.4 years ago by ▴ 780 • written 4.4 years ago by ▴ 10
6
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5
replies
1.9k
views
a problem of package ""
GEO GEOquery
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 20
2
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3
replies
1.7k
views
Problem about Geoquery
GEO GEOquery
4.4 years ago sheldon19931016 ▴ 20
7
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5
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7.3k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 10.4 years ago by 21k
0
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5
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4.5k
views
assayData: 0 features
geoquery
updated 4.7 years ago by ▴ 10 • written 10.1 years ago by ▴ 230
3
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4
replies
2.0k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 4.8 years ago by 21k • written 4.8 years ago by ▴ 20
3
votes
1
reply
1.5k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
0
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2
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3.1k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 5.0 years ago by 1.6k • written 5.0 years ago by • 0
6
votes
3
replies
2.1k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 5.4 years ago by 21k • written 5.4 years ago by ▴ 40
1
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1
reply
1.7k
views
Table expression data from GEO file
GEO expression GEOquery
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by • 0
5
votes
5
replies
1.8k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 840
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1
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1.5k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 5.8 years ago by ★ 13k • written 5.8 years ago by • 0
0
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3
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1.6k
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GEOquery and Feature data
GEOquery featureNames
updated 6.0 years ago by 21k • written 6.0 years ago by • 0
0
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3
replies
2.3k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 20
3
votes
2
replies
3.1k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 20
2
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1
reply
2.1k
views
Downloading a private GEO with GEOquery
GEOquery
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 760
0
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5
replies
2.9k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
0
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0
replies
1.3k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
3
votes
6
replies
4.3k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
6.5 years ago andy_shaps ▴ 10
1
vote
2
replies
1.8k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
3
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4
replies
2.0k
views
GEOquery:Get error sampleNames
geoquery
updated 6.8 years ago by 0 • written 6.9 years ago by ▴ 10
2
votes
2
replies
2.6k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 10
0
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2
replies
1.6k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.9 years ago cschot3 • 0
0
votes
0
replies
1.3k
views
Query based on PMIDs
SRAdb geoquery
6.9 years ago Deepak Tanwar ▴ 10
241 results • Page 1 of 5
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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