[BioC] GEOquery problem

Mon Jun 14 17:08:23 CEST 2010

Could that be because the soft file contains sequencing data instead of 
microarray data ?

On 06/14/2010 02:20 PM, David martin wrote:
> Sean,
> Here is the complete script.
>
>
>  > library(GEOquery)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: RCurl
> Loading required package: bitops
>  >
>  > data="/home/dvi/extdata/GSE21630_family.soft.gz"
>  > gse <- getGEO(filename=data,GSEMatrix=FALSE)
> Parsing....
> Found 47 entities...
> GPL9250 (1 of 47 entities)
> Error in read.table(file = file, header = header, sep = sep, quote =
> quote, :
> no lines available in input
>  > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0
>
>
>
>
>
>
>
>
>
>
> On 06/14/2010 12:52 PM, Sean Davis wrote:
>> On Mon, Jun 14, 2010 at 3:46 AM, David
>> martin<vilanew at gmail.com> wrote:
>>
>>> Sean,
>>> I have upgraded to GEOquery 2.13.2 but the problem is still there ??
>>> which
>>> version fixes that issue ?
>>>
>>>
>> It is working for me. Do you mind some sessionInfo() and the exact
>> code you
>> are using?
>>
>> Thanks,
>> Sean
>>
>>> gse = getGEO("GSE21630",GSEMatrix=FALSE)
>> File stored at:
>> /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE21630.soft
>>
>> Parsing....
>> Found 47 entities...
>> GPL9250 (1 of 47 entities)
>> GSM539835 (2 of 47 entities)
>> ....
>> GSM539879 (46 of 47 entities)
>> GSM539880 (47 of 47 entities)
>>> sessionInfo()
>> R version 2.12.0 Under development (unstable) (2010-04-30 r51866)
>> i386-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US/en_US/C/C/en_US/en_US
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets utils methods base
>>
>> other attached packages:
>> [1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.9.0
>>
>> loaded via a namespace (and not attached):
>> [1] XML_3.1-0
>>
>>
>>
>>> thanks
>>>
>>>
>>>
>>> On 06/10/2010 03:55 PM, Sean Davis wrote:
>>>
>>>> On Thu, Jun 10, 2010 at 9:01 AM, David
>>>> martin<vilanew at gmail.com> wrote:
>>>>
>>>> Sean,
>>>>> Yes you're right, that was a problem with file location but i still
>>>>> have
>>>>> a
>>>>> problem, see log file below....
>>>>>
>>>>> A turn around for me was:
>>>>>
>>>>> library(GEOquery)
>>>>>>
>>>>> Loading required package: Biobase
>>>>>
>>>>> Welcome to Bioconductor
>>>>>
>>>>> Vignettes contain introductory material. To view, type
>>>>> 'openVignette()'. To cite Bioconductor, see
>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>>
>>>>> Loading required package: RCurl
>>>>> Loading required package: bitops
>>>>>
>>>>>> data="extdata/GSE21630_family.soft.gz"
>>>>>> gse<- getGEO(filename=data,GSEMatrix=FALSE)
>>>>>>
>>>>> Parsing....
>>>>> Found 47 entities...
>>>>> GPL9250 (1 of 47 entities)
>>>>> Error in read.table(file = file, header = header, sep = sep, quote =
>>>>> quote,
>>>>> :
>>>>> no lines available in input
>>>>>
>>>>>
>>>> Hi, David.
>>>>
>>>> Yep. It's a bug. Thanks for the report. The change has been committed
>>>> to
>>>> the release and devel branches and should be available soon in the next
>>>> day
>>>> or so. If you need it sooner, you can checkout from svn.
>>>>
>>>> Sean
>>>>
>>>>
>>>>
>>>> sessionInfo()
>>>>>>
>>>>> R version 2.11.0 (2010-04-22)
>>>>> i686-pc-linux-gnu
>>>>>
>>>>> locale:
>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>>> [7] LC_PAPER=ca_AD.UTF-8 LC_NAME=C
>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>> [11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>>
>>>>> other attached packages:
>>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0
>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 06/09/2010 06:12 PM, James W. MacDonald wrote:
>>>>>
>>>>> Hi David,
>>>>>>
>>>>>> David martin wrote:
>>>>>>
>>>>>> It looks to me that there might some problem with softfiles. Did
>>>>>>> anybody came across a similar problem ??
>>>>>>>
>>>>>>>
>>>>>>> library(GEOquery)
>>>>>>> gse<- getGEO(filename =
>>>>>>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery"))
>>>>>>>
>>>>>>> Error in read.table(con, sep = "\t", header = FALSE, nrows =
>>>>>>> nseries) :
>>>>>>> invalid 'nlines' argument
>>>>>>> In addition: Warning messages:
>>>>>>> 1: In file(fname, "r") :
>>>>>>> file("") only supports open = "w+" and open = "w+b": using the
>>>>>>> former
>>>>>>> 2: In file(con, "r") :
>>>>>>> file("") only supports open = "w+" and open = "w+b": using the
>>>>>>> former
>>>>>>> 3: In file(fname, "r") :
>>>>>>> file("") only supports open = "w+" and open = "w+b": using the
>>>>>>> former
>>>>>>>
>>>>>>>
>>>>>> You have to point to a file that actually exists!
>>>>>>
>>>>>> > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")
>>>>>> [1] ""
>>>>>>
>>>>>> If I use the softfile in that directory, it works for me.
>>>>>>
>>>>>> > gse<- getGEO(filename =
>>>>>> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"),
>>>>>> GSEMatrix=FALSE)
>>>>>> Parsing....
>>>>>> Found 36 entities...
>>>>>> GPL96 (1 of 36 entities)
>>>>>> GPL97 (2 of 36 entities)
>>>>>> GSM11805 (3 of 36 entities)
>>>>>> GSM11810 (4 of 36 entities)
>>>>>> GSM11814 (5 of 36 entities)
>>>>>> GSM11815 (6 of 36 entities)
>>>>>> GSM11823 (7 of 36 entities)
>>>>>> GSM11827 (8 of 36 entities)
>>>>>> GSM11830 (9 of 36 entities)
>>>>>> GSM11832 (10 of 36 entities)
>>>>>> GSM12067 (11 of 36 entities)
>>>>>> GSM12069 (12 of 36 entities)
>>>>>> GSM12075 (13 of 36 entities)
>>>>>> GSM12078 (14 of 36 entities)
>>>>>> GSM12079 (15 of 36 entities)
>>>>>> GSM12083 (16 of 36 entities)
>>>>>> GSM12098 (17 of 36 entities)
>>>>>> GSM12099 (18 of 36 entities)
>>>>>> GSM12100 (19 of 36 entities)
>>>>>> GSM12101 (20 of 36 entities)
>>>>>> GSM12105 (21 of 36 entities)
>>>>>> GSM12106 (22 of 36 entities)
>>>>>> GSM12268 (23 of 36 entities)
>>>>>> GSM12269 (24 of 36 entities)
>>>>>> GSM12270 (25 of 36 entities)
>>>>>> GSM12274 (26 of 36 entities)
>>>>>> GSM12283 (27 of 36 entities)
>>>>>> GSM12287 (28 of 36 entities)
>>>>>> GSM12298 (29 of 36 entities)
>>>>>> GSM12299 (30 of 36 entities)
>>>>>> GSM12300 (31 of 36 entities)
>>>>>> GSM12301 (32 of 36 entities)
>>>>>> GSM12399 (33 of 36 entities)
>>>>>> GSM12412 (34 of 36 entities)
>>>>>> GSM12444 (35 of 36 entities)
>>>>>> GSM12448 (36 of 36 entities)
>>>>>>
>>>>>> > sessionInfo()
>>>>>> R version 2.11.0 Patched (2010-05-01 r51890)
>>>>>> i386-pc-mingw32
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_COLLATE=English_United States.1252
>>>>>> [2] LC_CTYPE=English_United States.1252
>>>>>> [3] LC_MONETARY=English_United States.1252
>>>>>> [4] LC_NUMERIC=C
>>>>>> [5] LC_TIME=English_United States.1252
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices datasets utils methods base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] tools_2.11.0
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Jim
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>>
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