Showing : geoquery • reset
1
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
0
votes
4
replies
746
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 6 months ago by 21k • written 6 months ago by • 0
0
votes
9
replies
830
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Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
7 months ago gallantk5 • 0
1
vote
5
replies
1.7k
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
0
votes
3
replies
596
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
0
votes
7
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1.4k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
10 months ago needNGS • 0
0
votes
1
reply
796
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
18 months ago Arianna • 0
0
votes
2
replies
1.0k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 22 months ago by 52k • written 22 months ago by • 0
0
votes
2
replies
825
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 22 months ago by • 0 • written 22 months ago by • 0
0
votes
1
reply
872
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 24 months ago by 67k • written 24 months ago by • 0
0
votes
1
reply
752
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
3
votes
2
replies
1.9k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.5 years ago by 4.1k • written 2.5 years ago by ▴ 10
0
votes
1
reply
842
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
1
vote
5
replies
1.5k
views
Can't read in CEL files
GEO GEOquery
2.6 years ago OE • 0
0
votes
2
replies
1.4k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.7 years ago Yugang • 0
2
votes
1
reply
3.4k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.9 years ago by ▴ 100 • written 2.9 years ago by • 0
5
votes
7
replies
2.7k
views
GEO series matrix empty
GEOquery GEO
2.9 years ago gs.123 ▴ 20
3
votes
2
replies
1.5k
views
GEOquery returning NAs as probe names
GEOquery
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 30
3
votes
23
replies
4.7k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.2 years ago array chip ▴ 420
1
vote
2
replies
3.0k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 10
0
votes
1
reply
2.6k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
2
votes
3
replies
1.7k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.2 years ago by ★ 13k • written 3.2 years ago by ▴ 50
6
votes
7
replies
2.8k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.2 years ago by 67k • written 3.2 years ago by ▴ 50
1
vote
1
reply
1.5k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.4 years ago by 67k • written 3.4 years ago by ▴ 50
1
vote
1
reply
1.9k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 3.5 years ago by 21k • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.0k
views
GEOquery
GEOquery
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by ▴ 10
6
votes
5
replies
1.6k
views
a problem of package ""
GEO GEOquery
updated 3.7 years ago by 16k • written 3.7 years ago by ▴ 20
2
votes
3
replies
1.4k
views
Problem about Geoquery
GEO GEOquery
3.7 years ago sheldon19931016 ▴ 20
7
votes
5
replies
6.8k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.7 years ago by 21k
0
votes
5
replies
4.1k
views
assayData: 0 features
geoquery
updated 3.9 years ago by ▴ 10 • written 9.4 years ago by ▴ 230
3
votes
4
replies
1.7k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 20
3
votes
1
reply
1.2k
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 4.1 years ago by 52k • written 4.1 years ago by • 0
0
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2
replies
2.6k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 4.3 years ago by 1.6k • written 4.3 years ago by • 0
6
votes
3
replies
1.7k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 40
1
vote
1
reply
1.4k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.8 years ago by ★ 3.4k • written 4.8 years ago by • 0
5
votes
5
replies
1.5k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.9 years ago by 67k • written 4.9 years ago by ▴ 840
0
votes
1
reply
1.3k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 5.0 years ago by ★ 13k • written 5.0 years ago by • 0
0
votes
3
replies
1.4k
views
GEOquery and Feature data
GEOquery featureNames
updated 5.2 years ago by 21k • written 5.2 years ago by • 0
0
votes
3
replies
2.0k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 5.3 years ago by 67k • written 5.3 years ago by ▴ 20
3
votes
2
replies
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 5.3 years ago by 67k • written 5.3 years ago by ▴ 20
2
votes
1
reply
1.7k
views
Downloading a private GEO with GEOquery
GEOquery
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 760
0
votes
5
replies
2.5k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.6 years ago by 67k • written 5.6 years ago by • 0
0
votes
0
replies
1.2k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
3
votes
6
replies
3.6k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.8 years ago andy_shaps ▴ 10
1
vote
2
replies
1.6k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
3
votes
4
replies
1.8k
views
GEOquery:Get error sampleNames
geoquery
updated 6.1 years ago by 0 • written 6.2 years ago by ▴ 10
2
votes
2
replies
2.3k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.1 years ago by 67k • written 6.1 years ago by ▴ 10
0
votes
2
replies
1.4k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.2 years ago cschot3 • 0
0
votes
0
replies
1.1k
views
Query based on PMIDs
SRAdb geoquery
6.2 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
3.0k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 20
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Comment: Identifying potentially associated gene set to drug response using GSVA by kl2023gege • 0
Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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