Aroma Affymetrix (v 2.5.0) installation dependencies

[Jay]

Dear Henrik

I am a consultant working with Laurent Malvert.
Many thanks for helping us with the aroma.affymetrix issue we have
been experiencing. Gladly this looks like being complete.
Whilst installing your recent release of aroma.affymetrix v2.5.0, I
encountered some dependencies and would like to confirm my findings
with you.

To update my current installation the software stack looks like.

R (v2.15)
BioConductor (v2.10)
aroma.light (v1.18.4)
aroma.affymetrix (v2.5.0)

Would you mind confirming these dependencies?


Kind regards,
Jay

[Henrik Bengtsson]

Hi.

Yes, installing aroma.affymetrix v2.5.0 with such dependencies should
work, if that is your question. Otherwise, I try to be as explicit as
possible in the DESCRIPTION files with what dependencies and their
versions aroma.affymetrix requires. Note also that aroma.affymetrix
only requires aroma.light and affxparser from Bioconductor.

/Henrik

>
>
> Kind regards,
> Jay
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
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[Henrik Bengtsson]

Hi,

On Mon, Aug 13, 2012 at 4:48 AM, Jay <jayangs...@gmail.com> wrote:
> Thanks a lot for your reply. I managed to install successfully and its
> working only in firefox. I am using Firefox v13.0.1. Unfortunately I need to
> make this work in Internet Explorer 7 or 8. I am getting few javascript
> error. Please see the screenshots. In the release note of version 2.4.5
> dated 03-02-2012, you mentioned "GENERALIZATION: As ChromosomeExplorer v3.3,
> the new ArrayExplorer v3.3 works with most common web browsers. See below.
> However, we still have problems getting ArrayExplorer to load the main
> spatial (PNG) image in Internet Explorer."

More up-to-date news on this are available via:

http://cran.r-project.org/web/packages/aroma.core/NEWS


>
> Is this the reason I am getting the error? Would you mind confirming these?

I never got a screenshot (please send cut'n'paste text messages if
possible), so I don't know what Javascript errors you get, so I cannot
confirm them, but...

> If possible, please suggest an alternative way to visualise in Internet
> explorer 7 or 8.

There are online demos of ArrayExplorer v3.4 and ChromosomeExplorer
v3.4 (which is what the most recent versions of aroma.* produces):

http://aroma-project.org/demos/

I've verified that ChromosomeExplorer v3.4 works with Internet
Explorer 7, 8, and 9 (on Windows 7 64-bit). ArrayExplorer v3.4
appears to only work with Internet Explorer 9.0. Support for older
versions of Internet Explorer (certainly v7) is not one of my top
priorities.

Cheers,

Henrik

>
> Thanks in advance.
>
> Kind regards,
> Jay
>
>

[Jay]

Hi Henrik,

Hope you are doing good. Firstly, thank you very much for your reply.

I am extremely sorry for not attaching the screenshot. I am attaching it now. Please do let me know if you have any issue viewing this jpeg.

Many thanks for confirming that currently ArrayExplorer v3.4 is only supported by Internet Explorer 9.0.


Thanks,
Jay

[Henrik Bengtsson]

Your screenshot tells me you are using an older version of
ArrayExplorer, cf. the header of
http://aroma-project.org/demos/reports/GSE8605/raw/ArrayExplorer.html

Also, those are not Javascript errors, but most likely rather due to
how you're incorporating the ArrayExplorer in that webpage.

/Henrik

>
>
>
> Thanks,