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, ...
- 2,656
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 ...
- 3,892
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 ...
- 9,442
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. ...
- 861
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
- 279
1
vote
Accepted
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 ...
- 575
1
vote
Extracting expression data in r from GEO and got a S4 object
Well, if you use a SOFT formatted files:
...
- 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 ...
- 19.5k
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 ...
- 2,739
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 ...
- 19.5k
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 ...
- 3,892
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