I have manually downloaded a series matrix file from GEO database in my machine. I wish to load this file in R Bioconductor. What command should I use?
Also, I was wondering if there is a package or command that can combine the expression values on multiple probes for the same gene?
The issue here is that getGEO(), when called on a GSEMatrix file, needs access to the GPL file as well. GEOquery normally then tries to go and download the GPL file if it is not available and it is not in this case as evidenced by the error:
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&view=full'
The easiest way to fix this problem is to use GEOquery once while connected to the internet and specifying a download location. Short of that, you can download the URL in the error message BY HAND and save it in the same directory as the GSEMatrix file with the filename "GPL96.soft". At that point, getGEO() can use the version stored locally (you'll need to specify the correct destdir).
Dear ayanava18,
try using the function getGEO() from the package 'GEOquery'.
for combination of multiple probes consider using command aggregate()
Hi Dimitri,
My objective is to load a PREVIOUSLY DOWLOADED GSE series matrix file into R. The file is saved in my working directory.
I am using the command :
gse2034 <- getGEO(filename='GSE2034.txt.gz')
but I am getting some error message.
And which error message are you getting? Please, also add the output of sessionInfo(). According to the vignette of the GEOquery package here, which I assumed you have read, it should be possible to load data from files. For example, it is mentioned:
# If you have network access, the more typical way to do this
# would be to use this:
# gds <- getGEO("GDS507")
gds <- getGEO(filename=system.file("extdata/GDS507.soft.gz",package="GEOquery"))
and later:
# If you have network access, the more typical way to do this
# would be to use this:
# gds <- getGEO("GSM11805")
gsm <- getGEO(filename=system.file("extdata/GSM11805.txt.gz",package="GEOquery"))
This is the Error message , I am getting:
Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&view=full'
In addition: Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
InternetOpenUrl failed: 'The operation timed out'
CODE
> gse2990 <- getGEO(filename='GSE2990_series_matrix.txt.gz')
OUTPUT
Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&view=full'
In addition: Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
InternetOpenUrl failed: 'The operation timed out'
BOTTOMLINE : I would like to know if there is any code by which I can load an ALREADY DOWNLOADED GSE Series Matrix file into R ( if the code I have used is wrong)
Sorry, I did not notice you had actually provided the code in another post. But the output of sessionInfo() is typically necessary when asking questions about problems running packages, since then people can know which version of the packages are you using and whether there might be a problem with the installation (see here). Thanks to Sean's response that may be not necessary anymore.
Tried your way:
> getGEO(filename="C:/Users/854661/Documents/GSE2990_series_matrix.txt") -> getSet
Getting the same thing:
Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&view=full'
In addition: Warning message:
In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
InternetOpenUrl failed: 'The operation timed out
On the other hand, if I try to load the .gz file ( the zipped one), I get this:
CODE
> getGEO(filename="C:/Users/854661/Documents/GSE2990_series_matrix.txt.gz") -> getSet
OUTPUT
Using locally cached version of GPL96 found here:
C:\Users\854661\AppData\Local\Temp\Rtmp2RK0dK/GPL96.soft
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
invalid 'nlines' argument
For working directory, I get this :
> getwd()
[1] "C:/Users/854661/Documents"
** The file is in my working directory- checked it
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Thank you very much Sean....