[BioC] vignette feedback - HowTo: Automated Querying of PubMed Data

[John Zhang]

>Dear Sir:
>
>Thank you for this R tool.  As I sometimes have a developer role, I 
>though I would give you some feedback.
>
> I recently installed BioConductor using 
>source("http://www.bioconductor.org/getBioC.R") and getBioC(libName = 
>"all").  Although I was suscessful in completing the vignette, "HowTo: 
> Automated Querying of PubMed Data", I spent quite a bit of time on the 
>step "library(hgu95a)"  

hgu95a data package is not available any more. We are going to replace hgu95a 
with hgu95av2 in the vignettes and elsewhere.

>
>First I got the no package error, so I tried hgu95av2 with the same 
>result.  Next I tried getBioC(libName = "hgu95av2") and got the error 
>that the library is not valid.  Finally I download the tar.gz file to my 
>disk and installed it using the R command.

getBioC is not for getting data packages. Data packages have to be obtained 
manually.

>
>I guess that hgu95a is no longer available, and probably its absence 
>affects only tens of genes.

Thank you for reporting the error.

>
>Sincerely,
>Lynn
>
>-- 
>Lynn Young * National Institutes of Health, USA
>CIT, MSC 5620; Bethesda, Maryland 20892-5620
>Phone: (301) 496-1137 * FAX: (301) 402-4544
>E-mail: lynny at helix.nih.gov
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084