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Geoquery
•
reset
0
votes
7
replies
351
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
26 days ago • updated 24 days ago
needNGS
• 0
0
votes
1
reply
464
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression
Bioconductor
GEOquery
MethylationArrayData
9 months ago
Arianna
• 0
0
votes
2
replies
675
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Ankita
• 0
0
votes
2
replies
575
views
Doubt about expression data as well as assay
GEOquery
ExpressionData
assay
SummarizedExperiment
ExpressionAtlas
updated 13 months ago by
pmadrigal
• 0 • written 13 months ago by
Kritikaverma2707
• 0
0
votes
1
reply
624
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Aleksandra
• 0
8
votes
4
replies
4.7k
views
GEOquery: 0 features in the gset object
geoquery
updated 17 months ago by
Fardad
• 0 • written 8.7 years ago by
alakatos
▴ 130
0
votes
1
reply
493
views
empty values when extracting beta values using the GEOquery
GSE61380
GEOquery
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
Carolin
• 0
7
votes
5
replies
6.1k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
written 8.9 years ago by
Sean Davis
21k
3
votes
2
replies
1.3k
views
Unable to download supplementary files from GSE146963 using GEOquery
GEOquery
updated 20 months ago by
shepherl
3.8k • written 20 months ago by
Durga
▴ 10
0
votes
1
reply
643
views
Regarding Installation of GEOquery
BiocManager
installation
GEOquery
updated 21 months ago by
Basti
▴ 780 • written 21 months ago by
surinder.chd90
• 0
1
vote
5
replies
1.1k
views
Can't read in CEL files
GEO
GEOquery
22 months ago
OE
• 0
0
votes
2
replies
961
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery
DEseq2
23 months ago
Yugang
• 0
1
vote
1
reply
2.4k
views
Error in downloading GEO Supplementary files
GEOquery
updated 2.1 years ago by
tcalvo
▴ 90 • written 2.1 years ago by
wasilewska.karolina
• 0
5
votes
7
replies
2.1k
views
GEO series matrix empty
GEOquery
GEO
2.2 years ago
gs.123
▴ 20
3
votes
2
replies
1.2k
views
GEOquery returning NAs as probe names
GEOquery
updated 2.3 years ago by
Sean Davis
21k • written 2.3 years ago by
John
▴ 30
3
votes
23
replies
3.8k
views
GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")
GEOquery
VROOM
2.4 years ago
array chip
▴ 420
1
vote
2
replies
2.4k
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 2.4 years ago by
Sean Davis
21k • written 2.4 years ago by
20yx17
▴ 10
0
votes
1
reply
2.1k
views
Data frame with 0 columns and 0 rows
GEOquery
updated 2.4 years ago by
Basti
▴ 780 • written 2.4 years ago by
墨
• 0
2
votes
3
replies
1.3k
views
Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery
CancerData
limma
RCy3
CancerInSilico
updated 2.4 years ago by
Steve Lianoglou
★ 13k • written 2.4 years ago by
Caitlin
▴ 50
6
votes
7
replies
2.2k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Caitlin
▴ 50
1
vote
1
reply
1.1k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Caitlin
▴ 50
1
vote
1
reply
1.4k
views
unable to find an inherited method for function ‘Table’ for signature ‘"GSE"
GEOquery
updated 2.8 years ago by
Sean Davis
21k • written 2.8 years ago by
pedram_torabian
▴ 10
0
votes
1
reply
857
views
GEOquery
GEOquery
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 years ago by
curiousmind007
▴ 10
6
votes
5
replies
1.2k
views
a problem of package ""
GEO
GEOquery
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
sheldon19931016
▴ 20
2
votes
3
replies
984
views
Problem about Geoquery
GEO
GEOquery
2.9 years ago
sheldon19931016
▴ 20
0
votes
5
replies
3.5k
views
assayData: 0 features
geoquery
updated 3.2 years ago by
H. Z. Amini
▴ 10 • written 8.6 years ago by
Ed Siefker
▴ 230
3
votes
4
replies
1.3k
views
when using getGEO() from GEOquery, an error happened : a file does not exist
GEOquery
projectR
updated 3.2 years ago by
Sean Davis
21k • written 3.2 years ago by
jing
▴ 20
3
votes
1
reply
950
views
Limma: extend reading raw Illumina files, with Gene Omnbus Expression formats
beadarray
GSE22247
limma
GEOquery
IlluminaChip
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
bastien_chassagnol
• 0
0
votes
2
replies
1.8k
views
Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
software error
GEOquery
updated 3.5 years ago by
Laurent Gatto
1.6k • written 3.5 years ago by
zhangzhuo77
• 0
6
votes
3
replies
1.4k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 3.9 years ago by
Sean Davis
21k • written 3.9 years ago by
fabian
▴ 40
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
lsbew
• 0
5
votes
5
replies
1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools
huex10sttranscriptcluster.db
affymetrix
Geoquery
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
svlachavas
▴ 830
0
votes
1
reply
999
views
I have installed bioconductor, R still asks me to install it
bioconductor
biocLite
GEOquery
package
updated 4.3 years ago by
Steve Lianoglou
★ 13k • written 4.3 years ago by
luhan.ni
• 0
0
votes
3
replies
1.0k
views
GEOquery and Feature data
GEOquery
featureNames
updated 4.5 years ago by
Sean Davis
21k • written 4.5 years ago by
ekl
• 0
0
votes
3
replies
1.7k
views
When applying rma to featureset get error: 'package' must be of length 1
oligo
biobase
GEOquery
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 20
3
votes
2
replies
2.3k
views
Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
oligo
GEOquery
ExpressionSet
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
salamandra
▴ 20
2
votes
1
reply
1.3k
views
Downloading a private GEO with GEOquery
GEOquery
updated 4.6 years ago by
Sean Davis
21k • written 4.6 years ago by
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
2.0k
views
Install a custom CDF file
makecdf
RMA
annotation
biobase
GEOquery
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
Seymoo
• 0
0
votes
0
replies
948
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
andy_shaps
▴ 10
3
votes
6
replies
2.9k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
5.0 years ago
andy_shaps
▴ 10
1
vote
2
replies
1.3k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma
microarray
GEOquery
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
pgurkirat
• 0
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
ustcxyf
▴ 10
2
votes
2
replies
2.1k
views
geGeo error - Error in .subset2(x, i) : subscript out of bounds
geoquery
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
yurigorelik
▴ 10
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
5.4 years ago
cschot3
• 0
0
votes
0
replies
942
views
Query based on PMIDs
SRAdb
geoquery
5.4 years ago
Deepak Tanwar
▴ 10
5
votes
12
replies
2.6k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
mahm
▴ 20
2
votes
3
replies
1.6k
views
Filtering the probe set ids from GSE file
geoquery
GSE
5.7 years ago
mahm
▴ 20
3
votes
11
replies
2.4k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression
geoquery
GSE
bioconductor
microarray
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
mahm
▴ 20
3
votes
2
replies
1.8k
views
Installing GEOQuery failed with conda
geoquery
anaconda
libxml2
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
261092095
▴ 10
0
votes
1
reply
1.3k
views
question about getGEO function
geoquery
5.7 years ago
maryam.sabet
• 0
50 results • Page
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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