Showing : GEOquery • reset
4
votes
8
replies
8.3k
views
getGEO - cannot Open URL issue
getGEO R GEOquery
10.1 years ago alptaciroglu ▴ 50
2
votes
4
replies
3.9k
views
getGEO function not identifying local file
geoquery getGEO
10.1 years ago Prasanth ▴ 20
1
vote
3
replies
3.7k
views
How to use expression set object to select genes using different gene selection methods
microarray biobase geoquery
updated 10.1 years ago by ▴ 840 • written 10.1 years ago by ▴ 10
0
votes
4
replies
4.1k
views
GEOquery: Error Message
geoquery error
updated 10.2 years ago by ▴ 10 • written 10.3 years ago by ▴ 130
8
votes
4
replies
6.2k
views
GEOquery: 0 features in the gset object
geoquery
updated 2.9 years ago by • 0 • written 10.2 years ago by ▴ 130
5
votes
14
replies
20k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 10.3 years ago by 21k • written 10.3 years ago by ▴ 10
0
votes
3
replies
1.6k
views
namespace problem running GEOquery and justRMA in same session
affy geoquery
10.4 years ago Ty Thomson ▴ 100
2
votes
4
replies
1.9k
views
GEOquery: Missing featureNames after creating expression set from series matrix file
geoquery
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 10
1
vote
1
reply
2.0k
views
Error in Package GEOquery
geoquery error R microarray
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 20
2
votes
3
replies
3.3k
views
how to get all information of a platform for all samples using GEOquery
geoquery r
updated 10.6 years ago by 21k • written 10.6 years ago by ▴ 80
2
votes
13
replies
3.6k
views
SCAN.UPC: exception thrown when loading GEOQuery
scan.upc geoquery rcurl
10.8 years ago lep ▴ 90
0
votes
4
replies
1.9k
views
error reading GSE file
GEOquery GEOquery
updated 10.8 years ago by • 0 • written 14.3 years ago by ▴ 570
0
votes
2
replies
1.5k
views
GEOquery: How to use the tryCatch
r trycatch geoquery
updated 10.9 years ago by ★ 3.4k • written 10.9 years ago by • 0
1
vote
3
replies
6.4k
views
Geoquery: How to Continue Code Execution on Error
geoquery
updated 10.9 years ago by ★ 3.4k • written 10.9 years ago by • 0
0
votes
1
reply
1.4k
views
Incomplete dataset download from GEO
geoquery
updated 10.9 years ago by 21k • written 10.9 years ago by • 0
0
votes
1
reply
908
views
Determining and separating Affy Chips from GEOquery?
geoquery affy
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 20
3
votes
1
reply
2.8k
views
Processing RAW CEL files from GEO
CEL RAW geoquery readaffy
updated 11.0 years ago by 21k • written 11.0 years ago by ▴ 20
0
votes
7
replies
3.9k
views
Normalizing Expressionset Exprs without Raw CEL files
geoquery normalization
updated 11.0 years ago by ▴ 600 • written 11.0 years ago by ▴ 20
0
votes
1
reply
989
views
platform probes set ID microarray
microarray geoquery
updated 11.0 years ago by 25k • written 11.0 years ago by • 0
1
vote
1
reply
1.6k
views
Compare Row.names and ID from GSE datasets
geoquery GSE identical row.names
updated 11.1 years ago by 21k • written 11.1 years ago by ▴ 20
3
votes
3
replies
6.4k
views
Annotation from Submitter GPL in GSE dataset
annotation geoquery
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 20
0
votes
2
replies
4.9k
views
getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 11.2 years ago by ▴ 80 • written 11.2 years ago by ▴ 30
0
votes
6
replies
3.5k
views
processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 11.3 years ago by 21k • written 11.3 years ago by ▴ 190
0
votes
2
replies
1.3k
views
GEOquery not parsing GSE expression sets
GEOquery GEOquery
updated 11.3 years ago by 21k • written 11.3 years ago by ▴ 10
0
votes
1
reply
1.8k
views
GEOquery error when retrieving raw files
GEOquery GEOquery
updated 11.7 years ago by 21k • written 11.7 years ago by ▴ 110
0
votes
3
replies
1.4k
views
Analysing Affy data with limma
limma GEOquery limma GEOquery
updated 11.9 years ago by 68k • written 11.9 years ago by ▴ 240
0
votes
1
reply
2.7k
views
Meta data for gene from GEO
Annotation gpls GEOquery GEOmetadb Annotation gpls GEOquery GEOmetadb
updated 11.9 years ago by 21k • written 11.9 years ago by ▴ 200
0
votes
0
replies
2.1k
views
Fw: Meta data for gene from GEO
Annotation gpls GEOquery GEOmetadb Annotation gpls GEOquery GEOmetadb
11.9 years ago rohan bareja ▴ 200
0
votes
4
replies
2.8k
views
Meta data for gene from GEO
GEOquery GEOmetadb GEOquery GEOmetadb
updated 11.9 years ago by 21k • written 11.9 years ago by ★ 13k
0
votes
4
replies
22k
views
Unable to find an inherited method for function ‘exprs’
Biobase GEOquery virtualArray Biobase GEOquery virtualArray
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ▴ 210
0
votes
0
replies
913
views
GEOquery: incomplete feature data from GPL soft file
Annotation GEOquery Annotation GEOquery
12.3 years ago Sean Davis 21k
0
votes
0
replies
1.7k
views
GEOquery: incomplete feature data from GPL soft file
Annotation GEOquery Annotation GEOquery
12.4 years ago Renaud Gaujoux ▴ 170
0
votes
5
replies
1.8k
views
GEOquery and Sample Subsets
GEOquery GEOquery
updated 12.4 years ago by 21k • written 12.4 years ago by ▴ 750
0
votes
5
replies
2.4k
views
XML package - 500 internal server error
GEOquery ArrayExpress GEOquery ArrayExpress
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 740
0
votes
2
replies
2.2k
views
Error in getGEO command with GSEMatrix=TRUE
GEOquery GEOquery
updated 12.6 years ago by 21k • written 12.6 years ago by ▴ 40
0
votes
5
replies
1.9k
views
getGEO error
GEOquery GEOquery
updated 12.8 years ago by 21k • written 12.8 years ago by ▴ 440
0
votes
4
replies
2.3k
views
GEOquery getGEO error in read.table
Microarray GEOquery Microarray GEOquery
updated 12.8 years ago by ▴ 160 • written 12.8 years ago by ▴ 210
0
votes
0
replies
808
views
GEO newbie search question
limma GEOquery limma GEOquery
12.9 years ago Sean Davis 21k
0
votes
0
replies
961
views
Fw: download GSE data with GEOquery - Ignore this message
GEOquery GEOquery
13.0 years ago carol white ▴ 680
0
votes
0
replies
1.2k
views
download GSE data with GEOquery
GEOquery GEOquery
13.0 years ago carol white ▴ 680
0
votes
1
reply
2.2k
views
GEOquery, GSEMatrix parameter and lifecycle of GEO series data
GO Biobase PROcess GEOquery GO Biobase PROcess GEOquery
updated 13.4 years ago by 21k • written 13.4 years ago by ▴ 440
0
votes
3
replies
2.1k
views
GEOquery, GSEMatrix parameter and lifecycle of GEO series data
PROcess GEOquery PROcess GEOquery
13.4 years ago Gustavo Fernández Bayón ▴ 440
0
votes
1
reply
1.1k
views
GEOquery install problem with openSUSE 11.4 and R 2.15
GEOquery GEOquery
updated 13.4 years ago by 21k • written 13.4 years ago by ▴ 60
2
votes
15
replies
10k
views
GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")
GEOquery GEOquery
updated 13.4 years ago by 68k • written 13.4 years ago by ★ 13k
0
votes
4
replies
3.3k
views
GEOquery loading error
hgu133plus2 GEOquery BiocInstaller hgu133plus2 GEOquery BiocInstaller
updated 13.4 years ago by ★ 8.2k • written 13.4 years ago by ★ 13k
0
votes
1
reply
3.1k
views
GEOquery package
GEOquery GEOquery
updated 13.5 years ago by ★ 8.2k • written 13.5 years ago by ▴ 30
0
votes
6
replies
1.6k
views
installation error of a bioconductor package in my workspace
GEOquery GEOquery
updated 13.5 years ago by ▴ 680 • written 13.5 years ago by ★ 8.2k
0
votes
5
replies
1.9k
views
installation error of a bioconductor package in my workspace
GEOquery GEOquery
13.5 years ago carol white ▴ 680
0
votes
1
reply
887
views
beadarray vignette has broken code in R2.14.1?
illuminaHumanv2 limma GEOquery beadarray illuminaHumanv2 limma GEOquery beadarray
updated 13.7 years ago by ▴ 20 • written 13.7 years ago by ★ 8.2k
0
votes
0
replies
813
views
beadarray vignette has broken code in R2.14.1?
illuminaHumanv2 limma GEOquery beadarray illuminaHumanv2 limma GEOquery beadarray
13.7 years ago Henriquez, Nick ▴ 20
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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