[BioC] MIAME object and abstract

[Daniel Brewer]

Sorry about that.  Here is an example:

> exptData <- new("MIAME",title="Integration of gene expression
profiling and clinical variables to predict prostate carcinoma
recurrence after radical
prostatectomy.",pubMedIds="15948174",name="Andrew J.
Stephenson",abstract="BACKGROUND: Gene expression profiling of prostate
carcinoma offers an alternative means to distinguish aggressive tumor
biology and may improve the accuracy of outcome prediction for patients
with prostate carcinoma treated by radical prostatectomy. METHODS: Gene
expression differences between 37 recurrent and 42 nonrecurrent primary
prostate tumor specimens were analyzed by oligonucleotide microarrays.
Two logistic regression modeling approaches were used to predict
prostate carcinoma recurrence after radical prostatectomy. One approach
was based exclusively on gene expression differences between the two
classes. The second approach integrated prognostic gene variables with a
validated postoperative predictive model based on standard variables
(nomogram). The predictive accuracy of these modeling approaches was
evaluated by leave-one-out cross-validation (LOOCV) and compared with
the nomogram. RESULTS: The modeling approach using gene variables alone
accurately classified 59 (75%) tissue samples in LOOCV, a classification
rate substantially higher than expected by chance. However, this
predictive accuracy was inferior to the nomogram (concordance index,
0.75 vs. 0.84, P = 0.01). Models combining clinical and gene variables
accurately classified 70 (89%) tissue samples and the predictive
accuracy using this approach (concordance index, 0.89) was superior to
the nomogram (P = 0.009) and models based on gene variables alone (P <
0.001). Importantly, the combined approach provided a marked improvement
for patients whose nomogram-predicted likelihood of disease recurrence
was in the indeterminate range (7-year disease progression-free
probability, 30-70%; concordance index, 0.83 vs. 0.59, P = 0.01).
CONCLUSIONS: Integration of gene expression signatures and clinical
variables produced predictive models for prostate carcinoma recurrence
that perform significantly better than those based on either clinical
variables or gene expression information alone.")
+")

> abstract(exptData)
[1] "BACKGROUND: Gene expression profiling of prostate carcinoma offers
an alternative means to distinguish aggressive tumor biology and may
improve the accuracy of outcome prediction for patients with prostate
carcinoma treated by radical prostatectomy. METHODS: Gene expression
differences between 37 recurrent and 42 nonrecurrent primary prostate
tumor specimens were analyzed by oligonucleotide microarrays. Two
logistic regression modeling approaches were used to predict prostate
carcinoma recurrence after radical prostatectomy. One approach was based
exclusively on gene expression differences between the two classes. The
second approach integrated prognostic gene variables with a validated
postoperative predictive model based on standard variables (nomogram).
The predictive accuracy of these)\n"

Not sure why you have to add the extra ").

> sessionInfo()
R version 2.5.1 (2007-06-27)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
 Biobase
"1.14.1"


Thanks

Dan

Robert Gentleman wrote:
> Hi Daniel,
>   The posting guide does ask for reproducible examples, and for the
> rather important reason that it would help someone try to help you.
> Could you please include things like sessionInfo and small
> self-contained examples?
> 
>  In the present case, I doubt that the abstract is truncated, but rather
> that the printed version is, but without a lot more detail from you, I
> wouldn't know.
> 
>   best wishes
>     Robert
> 
> 
> Daniel Brewer wrote:
>> I am creating a MIAME object to include in an ExpressionSet as
>> experiment data.  My question is regards the abstract field.  When I try
>> to enter an abstract it cuts it short.  I assume this is because a
>> string can only be so long in R or something with my readline
>> implementation.
>>
>> Has anyone else this problem?  How do you over come it?
>>
>> Thanks
>>
> 

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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