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Showing :
GEOquery
•
reset
0
votes
2
replies
71
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery
DEseq2
4 days ago • updated 3 days ago
Yugang
• 0
0
votes
1
reply
105
views
Error in downloading GEO Supplementary files
GEOquery
updated 8 weeks ago by
tcalvo
▴ 70 • written 8 weeks ago by
wasilewska.karolina
• 0
5
votes
7
replies
383
views
GEO series matrix empty
GEOquery
GEO
12 weeks ago • updated 10 weeks ago
gs.123
▴ 20
3
votes
2
replies
286
views
GEOquery returning NAs as probe names
GEOquery
updated 4 months ago by
Sean Davis
21k • written 4 months ago by
John
▴ 30
3
votes
23
replies
1.1k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery
VROOM
5 months ago
array chip
▴ 420
1
vote
2
replies
439
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 5 months ago by
Sean Davis
21k • written 5 months ago by
20yx17
▴ 10
0
votes
1
reply
471
views
Data frame with 0 columns and 0 rows
GEOquery
updated 5 months ago by
Basti
▴ 280 • written 5 months ago by
墨
• 0
2
votes
3
replies
309
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 6 months ago by
Steve Lianoglou
13k • written 6 months ago by
Caitlin
▴ 50
6
votes
7
replies
664
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 6 months ago by
James W. MacDonald
59k • written 6 months ago by
Caitlin
▴ 50
1
vote
1
reply
433
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 8 months ago by
James W. MacDonald
59k • written 8 months ago by
Caitlin
▴ 50
1
vote
1
reply
224
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 10 months ago by
Sean Davis
21k • written 10 months ago by
pedram_torabian
▴ 10
0
votes
1
reply
295
views
GEOquery
GEOquery
updated 11 months ago by
Basti
▴ 280 • written 11 months ago by
curiousmind007
• 0
6
votes
5
replies
440
views
a problem of package ""
GEO
GEOquery
updated 11 months ago by
Hervé Pagès
15k • written 11 months ago by
sheldon19931016
▴ 20
2
votes
3
replies
294
views
Problem about Geoquery
GEO
GEOquery
11 months ago
sheldon19931016
▴ 20
7
votes
3
replies
4.0k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
7.0 years ago • updated 10 months ago
Sean Davis
21k
0
votes
5
replies
1.7k
views
assayData: 0 features
geoquery
updated 14 months ago by
H. Z. Amini
• 0 • written 6.7 years ago by
Ed Siefker
▴ 230
3
votes
4
replies
553
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery
projectR
updated 15 months ago by
Sean Davis
21k • written 15 months ago by
jing
▴ 20
3
votes
1
reply
318
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray
GSE22247
limma
GEOquery
IlluminaChip
updated 17 months ago by
Gordon Smyth
45k • written 17 months ago by
bastien_chassagnol
• 0
0
votes
2
replies
571
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error
GEOquery
updated 19 months ago by
Laurent Gatto
1.5k • written 19 months ago by
zhangzhuo77
• 0
6
votes
3
replies
530
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 23 months ago by
Sean Davis
21k • written 23 months ago by
fabian
▴ 40
1
vote
1
reply
308
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 2.1 years ago by
Robert Castelo
★ 2.8k • written 2.1 years ago by
lsbew
• 0
4
votes
5
replies
485
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools
huex10sttranscriptcluster.db
affymetrix
Geoquery
updated 2.1 years ago by
James W. MacDonald
59k • written 2.1 years ago by
svlachavas
▴ 780
0
votes
1
reply
417
views
I have installed bioconductor, R still asks me to install it
bioconductor
biocLite
GEOquery
package
updated 2.3 years ago by
Steve Lianoglou
13k • written 2.3 years ago by
luhan.ni
• 0
0
votes
3
replies
355
views
GEOquery and Feature data
GEOquery
featureNames
updated 2.5 years ago by
Sean Davis
21k • written 2.5 years ago by
ekl
• 0
0
votes
3
replies
786
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
salamandra
▴ 20
2
votes
2
replies
983
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo
GEOquery
ExpressionSet
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
salamandra
▴ 20
2
votes
1
reply
474
views
Downloading a private GEO with GEOquery
GEOquery
updated 2.6 years ago by
Sean Davis
21k • written 2.6 years ago by
Lluís Revilla Sancho
▴ 660
0
votes
5
replies
1.1k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 2.9 years ago by
James W. MacDonald
59k • written 2.9 years ago by
Seymoo
• 0
0
votes
0
replies
414
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 3.0 years ago by
James W. MacDonald
59k • written 3.0 years ago by
andy_shaps
▴ 10
3
votes
6
replies
1.6k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
3.0 years ago
andy_shaps
▴ 10
1
vote
2
replies
569
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma
microarray
GEOquery
updated 3.1 years ago by
James W. MacDonald
59k • written 3.1 years ago by
pgurkirat
• 0
3
votes
4
replies
881
views
GEOquery:Get error sampleNames
geoquery
updated 3.3 years ago by
Bioconductor Community
0 • written 3.5 years ago by
ustcxyf
▴ 10
2
votes
2
replies
1.4k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 3.4 years ago by
James W. MacDonald
59k • written 3.4 years ago by
yurigorelik
▴ 10
0
votes
2
replies
628
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
3.5 years ago
cschot3
• 0
0
votes
0
replies
485
views
Query based on PMIDs
SRAdb
geoquery
3.5 years ago
Deepak Tanwar
▴ 10
5
votes
12
replies
1.4k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 3.7 years ago by
Sean Davis
21k • written 3.7 years ago by
mahm
▴ 20
2
votes
3
replies
782
views
Filtering the probe set ids from GSE file
geoquery
GSE
3.7 years ago
mahm
▴ 20
3
votes
11
replies
1.2k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression
geoquery
GSE
bioconductor
microarray
updated 3.7 years ago by
Sean Davis
21k • written 3.7 years ago by
mahm
▴ 20
3
votes
2
replies
903
views
Installing GEOQuery failed with conda
geoquery
anaconda
libxml2
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
261092095
▴ 10
0
votes
1
reply
807
views
question about getGEO function
geoquery
3.8 years ago
maryam.sabet
• 0
0
votes
1
reply
469
views
GEOquery install problem
geoquery
3.8 years ago
261092095
▴ 10
3
votes
5
replies
1.3k
views
getGEO function doesn't download the expression data
geoquery
updated 3.8 years ago by
Axel Klenk
▴ 990 • written 3.8 years ago by
fwere
▴ 10
0
votes
4
replies
713
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 4.0 years ago by
Sean Davis
21k • written 4.0 years ago by
Didi
▴ 10
1
vote
4
replies
1.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 4.1 years ago by
Sean Davis
21k • written 4.1 years ago by
arbet003
▴ 10
1
vote
2
replies
689
views
Error when Creating Expression Set from Geo Set
geoquery
4.1 years ago
dmm204
• 0
2
votes
2
replies
743
views
getGEO from GEOquery doesn't return probesets
geoquery
getgeo
probeset
updated 4.1 years ago by
James W. MacDonald
59k • written 4.1 years ago by
dnedveck
• 0
3
votes
2
replies
1.8k
views
getGEO error when trying to download a series matrix file
GEOquery
getGEO
4.2 years ago
rubi
▴ 100
2
votes
3
replies
688
views
GEO2R Gene Expression
geoquery
updated 4.2 years ago by
Sean Davis
21k • written 4.2 years ago by
nkline
▴ 10
1
vote
1
reply
646
views
GEOquery: Diagnosing SOFT file error
geoquery
geo data
geo
soft files
updated 4.2 years ago by
Sean Davis
21k • written 4.2 years ago by
supermanrocketboy
▴ 10
3
votes
4
replies
839
views
getGEO Error: Duplicate identifiers for rows
geoquery
getgeo
updated 4.2 years ago by
Sean Davis
21k • written 4.2 years ago by
umahajan
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
Yang Shi
• 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available
by
swbarnes2
★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
James W. MacDonald
59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
by
Rory Stark
★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
by
Yang Shi
• 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Use MulticoreParam under BatchtoolsParam
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
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