[BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....

[axel.klenk at actelion.com]

Dear Bas, 

I think you'll need to show us your original code, in particular what your 
'exprs' is
and how you have obtained it. If you have "extracted the expression 
values" from
an ExpressionSet ES like

x <- exprs(ES)

then x is a matrix and not a data.frame -- but then your output would look 
slightly
different. If you have done something like

x <- data.frame(exprs(ES))

I can reproduce your output, including rows that are all NA -- for 
rownames that
do not exist. 

So: how did you create 'exprs' and are you sure your rownames are ok?

Cheers,

 - axel


BTW: try

install.packages("fortunes")
library("fortunes")
fortune("dog")

to see why 'exprs' may not be a good name for your object... :-)



Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Bas Jansen <bjhjansen at gmail.com>
To:
Sebastian Thieme <thieme at mi.fu-berlin.de>
Cc:
bioconductor at r-project.org
Date:
03.01.2012 13:48
Subject:
Re: [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas 
data....
Sent by:
bioconductor-bounces at r-project.org



Dear Sebastian:

Thanks for your swift reply. It works, but only for the probe ID that
start with a character (only ~15 out of the > 100 probe IDs I want to
investigate). Those that start with a number report back with "<0
rows> (or 0-length row.names)". The motto for the New Year seems to be
'Solve a problem, only to find new ones'. Phew.

Kind regards,
Bas

On Tue, Jan 3, 2012 at 11:19 AM, Sebastian Thieme
<thieme at mi.fu-berlin.de> wrote:
> Hello,
>
> happy new year too =)
>
> you can use exprs[ rownames(exprs) %in% "gnf1h00499_at",] or exprs[
> rownames(exprs) %in% vectorOfNames,], where vectorOfNames is a list or
> a vector of the names you are looking for. Important is that the
> object you are search in has to be the first argument. If you want
> requesting a high number of names use lists instead of dataframes.
>
> best
>
> Basti
>
> 2012/1/3 Bas Jansen <bjhjansen at gmail.com>:
>> Dear fellow Bioconductor users:
>>
>> Happy New Year!
>> At the moment I am analyzing the GNF Atlas data. I retrieved the data
>> from the Gene Expression Omnibus using the package GEOquery, converted
>> it to an expressionSet and extracted the expression values. So now I
>> have a data frame from which I would like to extract the expression
>> values of > 100 probe IDs for 79 tissues. Thing is, if I use a single
>> probe ID, things go fine. However, whenever I use a string of probe
>> IDs, things go awry.
>>
>> See below:
>>
>> ***
>>> exprs[c("gnf1h00499_at"),]
>>              GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781 
GSM18774
>> gnf1h00499_at 5.770829 7.708739 5.161888 7.459432 6.332708 6.902074 
4.472488
>> (abbreviated for reasons of clarity)
>> ***
>>
>> As stated above: whenever I use a string of probe IDs (say, like 2
>> probe IDs), things go awry:
>>
>> ***
>>> exprs[c("gnf1h00499_at","gnf1h500_at"),]
>>              GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781 
GSM18774
>> gnf1h00499_at 5.770829 7.708739 5.161888 7.459432 6.332708 6.902074 
4.472488
>> NA                  NA       NA       NA       NA       NA       NA     
  NA
>> etc.
>> ***
>>
>> The gnf1h00500 probe is reported as NA, and I'm pretty sure it has
>> real expression values associated with it.
>> The following just works fine:
>>
>> ***
>>> exprs[c(1:20,30:70),]
>>            GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781 
GSM18774
>> 200000_s_at        0        0        0        0        0        0       
 0
>> 200001_at          0        0        0        0        0        0       
 0
>> 200002_at          0        0        0        0        0        0       
 0
>> 200003_s_at        0        0        0        0        0        0       
 0
>> etc.
>> ***
>>
>> So, how do I select rows on the basis of probe IDs? Or better yet:
>> what am I overlooking????
>>
>> Thanks & kind regards,
>> Bas
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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>> Search the archives: 
http://news.gmane.org/gmane.science.biology.informatics.conductor

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