[BioC] R: Help request about GEOquery and GSE9820

Manca Marco (PATH) m.manca at path.unimaas.nl
Thu Jul 16 23:40:42 CEST 2009

Dear Sean,

thank you for your kind and prompt answer.

I will check immediately my typo (the gse instead of gse9820)! =P

I have used this command
> gse9820<-getGEO("GSE9820", GSEMatrix=FALSE, destdir="C:\\Documents and Settings\\Marco Manca\\Mijn documenten\\GSE9820")

instead of
gse9820 <- getGEO('GSE9820')

because for some reason it wasn't importing/parsing the individual records and asking for
was giving a weird answer full of N/A signatures... However I will give it a shot later on and will give you a feedback on it.

Thank you again and keep up the great work!

Best regards,

Da: seandavi at gmail.com [seandavi at gmail.com] per conto di Sean Davis [sdavis2 at mail.nih.gov]
Inviato: giovedì 16 luglio 2009 13.36
A: Manca Marco (PATH)
Cc: Bioconductor Newsgroup
Oggetto: Re: Help request about GEOquery and GSE9820

On Thu, Jul 16, 2009 at 5:07 AM, Manca Marco (PATH) <m.manca at path.unimaas.nl<mailto:m.manca at path.unimaas.nl>> wrote:

Dear Sean,

good morning. I hope my email finds you well.

I apologize for incomodating you with a puny question about the use of your nice GEOquery packace, but I am quite a new user of it (Alberto Goldoni, who is a good friend of mine and a quite active member of Bioductor community whom you may know maybe) and I can not find a solution to an error message which is blocking me since one whole day. I hope in your understanding and support.

The case is as follows:
- I am trying to access the GSE9820 record on Gene Expression Omnibus.

- Using the command
> gse9820<-getGEO("GSE9820", GSEMatrix=FALSE, destdir="C:\\Documents and Settings\\Marco Manca\\Mijn documenten\\GSE9820")

I succeeded to acquire the data (I will omitt the result of the query gse9820 since it's some tens of thousands line which would just impair our commnication here)
- The command
> Table(GSMList(gse9820)[[1]])[1:5, ]
gives me the following output (which looks nice I think)
     ID_REF       VALUE
1 ILMN_10000  6.88027374
2 ILMN_10001 12.36707372
3 ILMN_10002  2.41509385
4 ILMN_10004 6.898955513
5 ILMN_10005 3.728241841

- But the command
> Columns(GSMList(gse9820)[[1]])[1:5, ]
gives me this (which looks nasty)
    Column                      Description
1    ID_REF
2     VALUE log2 normalized signal intensity
NA     <NA>                             <NA>
NA.1   <NA>                             <NA>
NA.2   <NA>                             <NA>

This looks this way because you asked for 5 column descriptions (1:5), but there are actually only two columns.  Doing:


will give a prettier answer, but the data is fine, either way.

- and in fact I can't manage to transform the data in an Expression set, the command
data.matrix <- log2(do.call("cbind", lapply(GSMList(gse), function(x) {
tab <- Table(x)
mymatch <- match(probesets, tab$ID_REF)
giving me the following error message
Error: object 'gse' not found
Error in GSMList(gse) :
 error in evaluating the argument 'object' in selecting a method for function 'GSMList'

This is a simple cut-and-paste problem.  You called your GSE "gse9820" and not "gse".

I am sure this is due to my short experience with your package but I can not find a solution (neither in my mind nor in the previous thread in the mailing list) alone and I am desperately stuck at this point. Could you give me any hint? Even just a suggestion of something to read to become able to find a solution my self would be a much apreciated help, if not a straight answer.

The more straightforward way of doing all this is to simply use the GEOquery default (at least for any newer version of GEOquery):

gse9820 <- getGEO('GSE9820')

This will return a __LIST__ of ExpressionSets and parses only the GSE Series Matrix file (so it is much faster than using GSEMatrix=FALSE).   Typically, there is only one member in that list (and that is the case for GSE9820, so to get a single ExpressionSet, do the following:

gse9820eSet <- gse9820[[1]]

Hope that helps.


Thank you in advance for your attention and support. My best regards,


Marco Manca, MD

University of Maastricht
Faculty of Health, Medicine and Life Science (FHML)
Cardiovascular Research Institute Maastricht (CARIM)
E-mail: m.manca at path.unimaas.nl<mailto:m.manca at path.unimaas.nl>

"Alma Mater Studiorum" University of Bologna
<<GC Descovich>> Atherosclerosis and Metabolic Diseases Study Centre
Dept. of Clinical Medicine and Applied Biotechnology
E-mail: m.manca at unibo.it<mailto:m.manca at unibo.it>
Website: http://spazioinwind.libero.it/marco_manca_1979

General Secretary of the International Society for Mathematical Models in Medicine
E-mail: medmath0 at yahoo.it<mailto:medmath0 at yahoo.it>

General Secretary of the Grupo Luso-Italiano de Arteriosclerose
E-mail: glia.secretary at gmail.com<mailto:glia.secretary at gmail.com>
Website: http://digilander.libero.it/Grupo_Luso_Italiano/

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