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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
Basti
▴ 530 • written 9 weeks ago by
Carolin
• 0
3
votes
2
replies
300
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 5 months ago by
shepherl
3.4k • written 5 months ago by
Durga
▴ 10
0
votes
1
reply
192
views
Regarding Installation of GEOquery
BiocManager
installation
GEOquery
updated 6 months ago by
Basti
▴ 530 • written 6 months ago by
surinder.chd90
• 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
tcalvo
▴ 80 • written 10 months ago by
wasilewska.karolina
• 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
Sean Davis
21k • written 12 months ago by
John
▴ 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
Sean Davis
21k • written 14 months ago by
20yx17
▴ 10
0
votes
1
reply
1.1k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 14 months ago by
Basti
▴ 530 • written 14 months ago by
墨
• 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
Steve Lianoglou
13k • written 14 months ago by
Caitlin
▴ 50
6
votes
7
replies
1.1k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 14 months ago by
James W. MacDonald
62k • written 14 months ago by
Caitlin
▴ 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
James W. MacDonald
62k • written 16 months ago by
Caitlin
▴ 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
Sean Davis
21k • written 18 months ago by
pedram_torabian
▴ 10
0
votes
1
reply
445
views
GEOquery
GEOquery
updated 20 months ago by
Basti
▴ 530 • written 20 months ago by
curiousmind007
• 0
6
votes
5
replies
644
views
a problem of package ""
GEO
GEOquery
updated 20 months ago by
Hervé Pagès
16k • written 20 months ago by
sheldon19931016
▴ 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
Sean Davis
21k
0
votes
5
replies
2.3k
views
assayData: 0 features
geoquery
updated 23 months ago by
H. Z. Amini
• 0 • written 7.4 years ago by
Ed Siefker
▴ 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
Sean Davis
21k • written 2.0 years ago by
jing
▴ 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
Gordon Smyth
47k • written 2.1 years ago by
bastien_chassagnol
• 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
Laurent Gatto
1.6k • written 2.3 years ago by
zhangzhuo77
• 0
6
votes
3
replies
753
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 2.6 years ago by
Sean Davis
21k • written 2.6 years ago by
fabian
▴ 40
1
vote
1
reply
594
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 2.8 years ago by
Robert Castelo
★ 3.0k • written 2.8 years ago by
lsbew
• 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
James W. MacDonald
62k • written 2.8 years ago by
svlachavas
▴ 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
Steve Lianoglou
13k • written 3.0 years ago by
luhan.ni
• 0
0
votes
3
replies
528
views
GEOquery and Feature data
GEOquery
featureNames
updated 3.2 years ago by
Sean Davis
21k • written 3.2 years ago by
ekl
• 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
James W. MacDonald
62k • written 3.2 years ago by
salamandra
▴ 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
James W. MacDonald
62k • written 3.3 years ago by
salamandra
▴ 20
2
votes
1
reply
717
views
Downloading a private GEO with GEOquery
GEOquery
updated 3.3 years ago by
Sean Davis
21k • written 3.3 years ago by
Lluís Revilla Sancho
▴ 700
0
votes
5
replies
1.4k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 3.6 years ago by
James W. MacDonald
62k • written 3.6 years ago by
Seymoo
• 0
0
votes
0
replies
595
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
andy_shaps
▴ 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
James W. MacDonald
62k • written 3.8 years ago by
pgurkirat
• 0
3
votes
4
replies
1.0k
views
GEOquery:Get error sampleNames
geoquery
updated 4.0 years ago by
Bioconductor Community
0 • written 4.2 years ago by
ustcxyf
▴ 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
James W. MacDonald
62k • written 4.1 years ago by
yurigorelik
▴ 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
Sean Davis
21k • written 4.4 years ago by
mahm
▴ 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
Sean Davis
21k • written 4.4 years ago by
mahm
▴ 20
3
votes
2
replies
1.2k
views
Installing GEOQuery failed with conda
geoquery
anaconda
libxml2
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
261092095
▴ 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
Axel Klenk
▴ 990 • written 4.5 years ago by
fwere
▴ 10
0
votes
4
replies
910
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 4.6 years ago by
Sean Davis
21k • written 4.7 years ago by
Didi
▴ 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
Sean Davis
21k • written 4.8 years ago by
arbet003
▴ 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
James W. MacDonald
62k • written 4.8 years ago by
dnedveck
• 0
50 results • Page
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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
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