Hi Anna-

I've shared the Dropbox location containing all the reads for the vignette with you.

I do want to ask what version of DiffBind you are using (perhaps send a sessionInfo() output?). The latest version (Bioconductor 2.13/DiffBind 1.8) has substantially new code for dba.count (using much less memory) -  you may want to check this out. Also, if memory is an issue in an older version, you can set the bLowMem option to TRUE in dba.count.

Cheers-
Rory

From: arusso <anna.russo@ieo.eu<mailto:anna.russo@ieo.eu>>
Date: Fri, 18 Oct 2013 14:47:12 +0200
To: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>>
Subject: Problems with DiffBind
Resent-From: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>>

Dear Dr Stark,
I'm a phd student at the IEO in Milan and I'm trying to use DiffBind package but I'm having some issues using the command dba.count.
I receive the segfault error that is also reported here http://grokbase.com/t/r/bioconductor/135ghztseq/bioc-diffbind-error-dba-count
I used the options you describe in your answer but the error still comes up.

So I wanted to ask you:
1. Can you suggest me other possible way to solve this problem?
2. Is it possible to have access to the bed files of tamoxifen dataset? In this way I can run the steps on your dataset and try to understand if there are problems with my dataset or not.

Thank you very much.
Kind regards,
Anna



***Please note that my email address has changed. Please update your records and address book***

Anna Russo
PhD student
IFOM-IEO Campus
via Adamello 16
20139 Milan (ITALY)
Email: anna.russo@ieo.eu<mailto:anna.russo@ieo.eu>
http://www.ifom-ieo-campus.it


NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for ...{{dropped:20}}

