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8 votes

Extracting expression data from GSE dataset downloaded from GEO

According to the manual, all you need to do is: library('GEOquery') gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE) As explanation, ...
aechchiki's user avatar
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5 votes

How do I pull singe cell RNA sequencing data from GEO database?

The simplest would be using a count matrix (at the end of the link you have shared, section "Supplementary file"). For example ...
haci's user avatar
  • 4,192
5 votes
Accepted

Gene symbol list for all protein coding genes in mice

If you want all known mouse protein coding genes, you can get the list from Ensembl's BioMart. First, select the mouse genome: Then, in "Filters" limit to protein coding genes only: And ...
terdon's user avatar
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3 votes
Accepted

Get Gene Expression Matrix from GEOquery

The answer to this really depends on the type of data you're retrieving from GEO. Microarray data sets should have a normalised matrix of expression values uploaded as part of the entry. ...
sjcockell's user avatar
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2 votes
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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values

Answered at biostars: https://www.biostars.org/p/9561238/#9561240 DESeq2 is meant for digital counts (RNA-seq and similar assays). Arrays are not supported, nor is the implemented method meaningful ...
ATpoint's user avatar
  • 1,440
1 vote

missing additional visits in GSE data

If it's not in there then you can either email the authors or just live with it. It is fully on the authors what you upload to NCBI. Nobody at NCBI checks the actual content of the uploads in terms of ...
ATpoint's user avatar
  • 1,440
1 vote
Accepted

How do you extract the full list of files in a GEO archive?

Unlikely that you will be able to get the original submission spreadsheet, but you can use Geofetch
Sam's user avatar
  • 149
1 vote
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coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist

Finally, I found it. filelist.txt file is accessible from the FTP server of the NCBI. For example for that specific microarray is stored here So there might be a ...
J. Doe's user avatar
  • 575
1 vote

Extracting expression data in r from GEO and got a S4 object

Well, if you use a SOFT formatted files: ...
Oka's user avatar
  • 203
1 vote

GEOquery errors due to list input

Use GSEMatrix=FALSE, the information you want appears to be in the soft file, rather than the matrix. Yes, this is moderately annoying since it means you need two ...
Devon Ryan's user avatar
  • 19.7k
1 vote

Comparing the gene expression data

It doesn't make sense to compare gene expression data from different studies unless you have a negative spiked-in control such as sequins. The most obvious thing you will need to do is normlizate the ...
SmallChess's user avatar
  • 2,729
1 vote

Comparing the gene expression data

There's going to be a batch effect between studies, so unless you have some sort of constant group that you can use for between-study normalization you're going to completely muck up your results from ...
Devon Ryan's user avatar
  • 19.7k
1 vote

Parsing gene expression value for a list of genes from GEO

GEO provides a GUI for this (just click on the "Analyze with GEO2 button"), you can even check/download the R/Bioconductor code used for the analyses. Basically you will create groups of ...
haci's user avatar
  • 4,192

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