[BioC] Need assistance with the file preparation for ChIPpeakAnno. (Jennifer Yang from University of California, Santa Barbara)

[Zhu, Lihua (Julie)]

Dear Jennifer,

Thank you very much for the positive feedback!

Regarding the annotation file you downloaded from fRNAdb, did you try to
save the first 6 columns as comma separated file (CSV)? If you still
encounter problem, please send the bioconductor list with error message to
seek input from those who are expert in read in data.

Best regards,

Julie


On 1/17/11 2:41 PM, "Chu-Ya (Jennifer) Yang" <chu-ya.yang at lifesci.ucsb.edu>
wrote:

> Dear Prof. Zhu,
> 
> I have been using ChIPpeakAnno to annotate my ChIP-seq data and found it
> is very helpful.  I also have tried to annotate my ChIP-seq data to
> custom annotation files in BED format and they also worked.
> 
> However, recently I encounter a problem when trying to annotate my
> ChIP-seq data to a custom annotation file in BED format downloaded from
> fRNAdb.  I think there is something wrong with the data frame of this
> file.  I tried different approaches and tricks, but nothing worked with
> this file when using read.table.  I also tried to export it to excel,
> add header, keep the first 6 columns (chromosome, start, end, name,
> score, and strand) and then saved it as Text (tab delimited) and then
> tried to input it into R again, but it still did not work.
> 
> Would you please help out with this question?  The size of the original
> BED file is around 7 Mb.  May I email you the file?
> 
> Thank you,
> 
> Jennifer