Showing : GEO • reset
2
votes
14
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2.7k
views
How to load scRNA-seq data from GEO
SingleCellExperiment GEO
13 days ago • updated 8 days ago petergrahamclark • 0
0
votes
1
reply
341
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
3
replies
749
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
10 months ago • updated 9 months ago gallantk5 • 0
0
votes
4
replies
1.1k
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 10 months ago by 21k • written 10 months ago by • 0
0
votes
9
replies
1.0k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
11 months ago • updated 10 months ago gallantk5 • 0
1
vote
10
replies
1.4k
views
Obtaining pheno data from CEL files
GEO affy
13 months ago Kurtis • 0
0
votes
1
reply
824
views
how to solve this error
DESeq2 GEO miRNAData
updated 24 months ago by ★ 4.8k • written 24 months ago by • 0
1
vote
5
replies
1.7k
views
Can't read in CEL files
GEO GEOquery
2.9 years ago OE • 0
5
votes
7
replies
3.0k
views
GEO series matrix empty
GEOquery GEO
3.2 years ago gs.123 ▴ 20
1
vote
2
replies
3.3k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 10
6
votes
7
replies
3.1k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 50
1
vote
3
replies
1.6k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
6
votes
5
replies
1.7k
views
a problem of package ""
GEO GEOquery
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 20
2
votes
3
replies
1.5k
views
Problem about Geoquery
GEO GEOquery
4.0 years ago sheldon19931016 ▴ 20
4
votes
2
replies
1.6k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
3
votes
4
replies
1.9k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.1 years ago hgalmoore • 0
2
votes
1
reply
3.6k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO oligo
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
5
votes
5
replies
4.1k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
4.7 years ago andrade4beatriz • 0
2
votes
2
replies
2.5k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Table expression data from GEO file
GEO expression GEOquery
updated 5.1 years ago by ★ 3.4k • written 5.1 years ago by • 0
0
votes
1
reply
1.7k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
vote
4
replies
1.6k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel GEO gene-expression
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
4
votes
5
replies
1.8k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Annotation Using GEOquery
Annotation GEO TXT
updated 5.5 years ago by 21k • written 5.5 years ago by • 0
0
votes
6
replies
1.7k
views
Opening Illumina HT12 V3.0 Data from GEO
limma normalization GEO
5.6 years ago FL512 • 0
3
votes
2
replies
1.5k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart geo software error ensembl
updated 5.9 years ago by ★ 6.6k • written 5.9 years ago by ▴ 10
0
votes
0
replies
1.2k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
3
votes
6
replies
4.1k
views
GEOquery: HTTP error 403
GEOquery GEO HTTP error 403
6.1 years ago andy_shaps ▴ 10
5
votes
12
replies
3.2k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.7 years ago by 21k • written 6.7 years ago by ▴ 20
1
vote
3
replies
1.2k
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 20
2
votes
6
replies
2.2k
views
error reading GSE using getGEO()
r geo getgeo
6.8 years ago jaleh.amo • 0
3
votes
2
replies
1.7k
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb GEO R bioconductor
updated 6.9 years ago by 21k • written 6.9 years ago by ▴ 20
1
vote
2
replies
2.0k
views
Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from …
limma microarray agilent microarrays GEO
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
votes
4
replies
1.9k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
7.0 years ago daniel.green • 0
1
vote
1
reply
1.7k
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 7.2 years ago by 21k • written 7.2 years ago by ▴ 10
3
votes
11
replies
5.0k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 7.3 years ago by 21k • written 8.1 years ago by • 0
3
votes
5
replies
6.2k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
7.3 years ago martinguerrerog89 ▴ 20
10
votes
7
replies
3.1k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 7.4 years ago by 21k • written 7.4 years ago by ▴ 60
1
vote
3
replies
2.9k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 7.6 years ago by 52k • written 7.6 years ago by • 0
0
votes
1
reply
1.9k
views
GEOquery download error
geoquery error message GEOquery GSE GEO
7.7 years ago Barah ▴ 20
1
vote
3
replies
1.8k
views
Getting gene annotation for a GEO dataset
geo
7.9 years ago yuvallb • 0
2
votes
2
replies
2.8k
views
GEOquery error in downloading SOFT files
geoquery getgeo GEO
8.5 years ago hzc363 ▴ 20
0
votes
1
reply
2.5k
views
Question about neqc and GEO illumina files
neqc illumina geo limma
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 30
2
votes
4
replies
1.9k
views
read bead-level data directly by lumi
bead-level GEO lumi
updated 9.2 years ago by ★ 6.6k • written 9.2 years ago by • 0
1
vote
2
replies
1.7k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray bead-level GEO lumi
updated 9.2 years ago by ★ 6.6k • written 9.2 years ago by • 0
0
votes
1
reply
1.3k
views
data handling from GSE22216 to exprSet object
GEO
updated 9.4 years ago by ★ 6.6k • written 9.4 years ago by ▴ 10
0
votes
5
replies
2.3k
views
collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 9.5 years ago by ★ 3.4k • written 9.5 years ago by • 0
0
votes
1
reply
1.5k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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Popular Question to Gordon Smyth 52k
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Scholar to James W. MacDonald 68k
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