Showing : geoquery • reset
1
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 4 weeks ago by 67k • written 4 weeks ago by • 0
0
votes
4
replies
660
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 5 months ago by 21k • written 5 months ago by • 0
0
votes
9
replies
767
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
6 months ago • updated 5 months ago gallantk5 • 0
1
vote
5
replies
1.5k
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery Bioconductor
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
0
votes
3
replies
544
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
7
replies
1.2k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
8 months ago needNGS • 0
0
votes
1
reply
756
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
17 months ago Arianna • 0
0
votes
2
replies
969
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 20 months ago by 52k • written 20 months ago by • 0
0
votes
2
replies
802
views
Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 21 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
849
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 22 months ago by 67k • written 22 months ago by • 0
0
votes
1
reply
713
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
3
votes
2
replies
1.8k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 2.3 years ago by 4.1k • written 2.3 years ago by ▴ 10
0
votes
1
reply
817
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
1
vote
5
replies
1.4k
views
Can't read in CEL files
GEO GEOquery
2.5 years ago OE • 0
0
votes
2
replies
1.3k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
2.6 years ago Yugang • 0
2
votes
1
reply
3.3k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.8 years ago by ▴ 100 • written 2.8 years ago by • 0
5
votes
7
replies
2.7k
views
GEO series matrix empty
GEOquery GEO
2.8 years ago gs.123 ▴ 20
3
votes
2
replies
1.5k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.9 years ago by 21k • written 3.0 years ago by ▴ 30
3
votes
23
replies
4.6k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
3.1 years ago array chip ▴ 420
1
vote
2
replies
2.9k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 10
0
votes
1
reply
2.5k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
2
votes
3
replies
1.6k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 3.1 years ago by ★ 13k • written 3.1 years ago by ▴ 50
6
votes
7
replies
2.7k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 50
1
vote
1
reply
1.4k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.3 years ago by 67k • written 3.3 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 3.4 years ago by 21k • written 3.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
GEOquery
GEOquery
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by ▴ 10
6
votes
5
replies
1.5k
views
a problem of package ""
GEO GEOquery
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 20
2
votes
3
replies
1.3k
views
Problem about Geoquery
GEO GEOquery
3.6 years ago sheldon19931016 ▴ 20
7
votes
5
replies
6.7k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.6 years ago by 21k
0
votes
5
replies
4.0k
views
assayData: 0 features
geoquery
updated 3.8 years ago by ▴ 10 • written 9.3 years ago by ▴ 230
3
votes
4
replies
1.6k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 3.9 years ago by 21k • written 3.9 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 4.0 years ago by 52k • written 4.0 years ago by • 0
0
votes
2
replies
2.5k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 4.2 years ago by 1.6k • written 4.2 years ago by • 0
6
votes
3
replies
1.7k
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 40
1
vote
1
reply
1.3k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.7 years ago by ★ 3.4k • written 4.7 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 4.7 years ago by 67k • written 4.7 years ago by ▴ 840
0
votes
1
reply
1.2k
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
0
votes
3
replies
1.3k
views
GEOquery and Feature data
GEOquery featureNames
updated 5.1 years ago by 21k • written 5.1 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 5.2 years ago by 67k • written 5.2 years ago by ▴ 20
3
votes
2
replies
2.7k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 20
2
votes
1
reply
1.6k
views
Downloading a private GEO with GEOquery
GEOquery
updated 5.2 years ago by 21k • written 5.2 years ago by ▴ 760
0
votes
5
replies
2.4k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 5.5 years ago by 67k • written 5.5 years ago by • 0
0
votes
0
replies
1.1k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 10
3
votes
6
replies
3.5k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
5.6 years ago andy_shaps ▴ 10
1
vote
2
replies
1.5k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
3
votes
4
replies
1.7k
views
GEOquery:Get error sampleNames
geoquery
updated 5.9 years ago by 0 • written 6.1 years ago by ▴ 10
2
votes
2
replies
2.3k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 6.0 years ago by 67k • written 6.0 years ago by ▴ 10
0
votes
2
replies
1.4k
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
6.1 years ago cschot3 • 0
0
votes
0
replies
1.1k
views
Query based on PMIDs
SRAdb geoquery
6.1 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 6.3 years ago by 21k • written 6.3 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation. Like most classical linear modeling procedures in statistics, limma uses a statistical model to represen…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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