Showing : GEOquery • reset
0
votes
1
reply
106
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 9 weeks ago by ▴ 530 • written 9 weeks ago by • 0
3
votes
2
replies
300
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 5 months ago by 3.4k • written 5 months ago by ▴ 10
0
votes
1
reply
192
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 6 months ago by ▴ 530 • written 6 months ago by • 0
1
vote
5
replies
338
views
Can't read in CEL files
GEO GEOquery
7 months ago OE • 0
0
votes
2
replies
344
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
8 months ago Yugang • 0
1
vote
1
reply
727
views
Error in downloading GEO Supplementary files
GEOquery
updated 10 months ago by ▴ 80 • written 10 months ago by • 0
5
votes
7
replies
950
views
GEO series matrix empty
GEOquery GEO
11 months ago gs.123 ▴ 20
3
votes
2
replies
522
views
GEOquery returning NAs as probe names
GEOquery
updated 12 months ago by 21k • written 12 months ago by ▴ 30
3
votes
23
replies
2.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery VROOM
14 months ago array chip ▴ 420
1
vote
2
replies
1.0k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 14 months ago by 21k • written 14 months ago by ▴ 10
0
votes
1
reply
1.1k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 14 months ago by ▴ 530 • written 14 months ago by • 0
2
votes
3
replies
543
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 14 months ago by 13k • written 14 months ago by ▴ 50
6
votes
7
replies
1.1k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 14 months ago by 62k • written 14 months ago by ▴ 50
1
vote
1
reply
631
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 16 months ago by 62k • written 16 months ago by ▴ 50
1
vote
1
reply
523
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 18 months ago by 21k • written 18 months ago by ▴ 10
0
votes
1
reply
445
views
GEOquery
GEOquery
updated 20 months ago by ▴ 530 • written 20 months ago by • 0
6
votes
5
replies
644
views
a problem of package ""
GEO GEOquery
updated 20 months ago by 16k • written 20 months ago by ▴ 20
2
votes
3
replies
450
views
Problem about Geoquery
GEO GEOquery
20 months ago sheldon19931016 ▴ 20
7
votes
5
replies
4.7k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 7.7 years ago by 21k
0
votes
5
replies
2.3k
views
assayData: 0 features
geoquery
updated 23 months ago by • 0 • written 7.4 years ago by ▴ 230
3
votes
4
replies
740
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery projectR
updated 24 months ago by 21k • written 2.0 years ago by ▴ 20
3
votes
1
reply
465
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray GSE22247 limma GEOquery IlluminaChip
updated 2.1 years ago by 47k • written 2.1 years ago by • 0
0
votes
2
replies
889
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error GEOquery
updated 2.3 years ago by 1.6k • written 2.3 years ago by • 0
6
votes
3
replies
753
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 2.6 years ago by 21k • written 2.6 years ago by ▴ 40
1
vote
1
reply
594
views
Table expression data from GEO file
GEO expression GEOquery
updated 2.8 years ago by ★ 3.0k • written 2.8 years ago by • 0
5
votes
5
replies
666
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 2.8 years ago by 62k • written 2.8 years ago by ▴ 800
0
votes
1
reply
568
views
I have installed bioconductor, R still asks me to install it
bioconductor biocLite GEOquery package
updated 3.0 years ago by 13k • written 3.0 years ago by • 0
0
votes
3
replies
528
views
GEOquery and Feature data
GEOquery featureNames
updated 3.2 years ago by 21k • written 3.2 years ago by • 0
0
votes
3
replies
1.1k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo biobase GEOquery
updated 3.2 years ago by 62k • written 3.2 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo GEOquery ExpressionSet
updated 3.3 years ago by 62k • written 3.3 years ago by ▴ 20
2
votes
1
reply
717
views
Downloading a private GEO with GEOquery
GEOquery
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 700
0
votes
5
replies
1.4k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 3.6 years ago by 62k • written 3.6 years ago by • 0
0
votes
0
replies
595
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 3.7 years ago by 62k • written 3.7 years ago by ▴ 10
3
votes
6
replies
2.1k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
3.7 years ago andy_shaps ▴ 10
1
vote
2
replies
712
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 3.8 years ago by 62k • written 3.8 years ago by • 0
3
votes
4
replies
1.0k
views
GEOquery:Get error sampleNames
geoquery
updated 4.0 years ago by 0 • written 4.2 years ago by ▴ 10
2
votes
2
replies
1.6k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 4.1 years ago by 62k • written 4.1 years ago by ▴ 10
0
votes
2
replies
775
views
GEOQuery bug, NCBI or package?
geoquery ncbi geo biobase
4.2 years ago cschot3 • 0
0
votes
0
replies
611
views
Query based on PMIDs
SRAdb geoquery
4.2 years ago Deepak Tanwar ▴ 10
5
votes
12
replies
1.7k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 20
2
votes
3
replies
1.0k
views
Filtering the probe set ids from GSE file
geoquery GSE
4.4 years ago mahm ▴ 20
3
votes
11
replies
1.5k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 20
3
votes
2
replies
1.2k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
0
votes
1
reply
955
views
question about getGEO function
geoquery
4.5 years ago maryam.sabet • 0
0
votes
1
reply
582
views
GEOquery install problem
geoquery
4.5 years ago 261092095 ▴ 10
3
votes
5
replies
1.6k
views
getGEO function doesn't download the expression data
geoquery
updated 4.5 years ago by ▴ 990 • written 4.5 years ago by ▴ 10
0
votes
4
replies
910
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 4.6 years ago by 21k • written 4.7 years ago by ▴ 10
1
vote
4
replies
1.2k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 4.8 years ago by 21k • written 4.8 years ago by ▴ 10
1
vote
2
replies
816
views
Error when Creating Expression Set from Geo Set
geoquery
4.8 years ago dmm204 • 0
2
votes
2
replies
904
views
getGEO from GEOquery doesn't return probesets
geoquery getgeo probeset
updated 4.8 years ago by 62k • written 4.8 years ago by • 0
50 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
on which data type limma::removeBatchEffect can be applyed?
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Awards • All
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