Next steps for Bioinformatics Students

Thank you @yvesgaetan, @aliciarepka and @Sarahrp for hosting! An excellent presentation!

Bioinformatics teams will start on 07/20. If everyone can get a head start on these deliverables, we can spend more time on the DGE and Functional Analysis Steps!

Here are links to the




When I click on First Set of deliverables, it brings up the Overall Project Document.

Please try now. Thanks for letting us know.

Thank you! It works now.

@ddas @Sarahrp
If I am an observer, are all of these tasks required for me as well like the QC and DV, I chose the observer position with the intention to only shadow the project and learn more about project management within bioinformatics. I have other commitments for the next couple of weeks, so I want to know what the observer role would be doing in the project specific to bioinformatics

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Hi @Trisha_N! Don’t worry, as an Observer you are not required to commit time or attention to the deliverables. You can decide day by day how active you wish to be on the team and are not required to complete tasks or attend meetings. However, as always, you will get out of the opportunity what you put into it!
In order to observe effectively I would recommend for you to stay as up-to-date as possible with the project steps. Hope this helps! I will make a note to discuss the Observer role further at our team meeting :wink:

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Yes this helps, thank you so much!

Hi, if I enter the project as a participant, am I allowed to request a position change to an observer during, say, the first or second week of the project? Additionally, how comfortable would we have to be using R before we step into the project? I would just like to gauge my readiness for the participant position.

Hi Abhinav, the learning resources & self-assessment should have answered your questions. You need to make the participant vs observer decision. We are not allowing changes this time because we have given you plenty of time & resources to figure out the best role for yourself.

For the batch correction step in the first set of deliverables, the document says that the metadata was provided for you, however, it was not attached.

For those of you getting a head start, here is a link to the appropriate metadata file:
https://drive.google.com/file/d/1ccnA95O86VfPVIE9hME88CEaOfatz2oh/view?usp=sharing

Please note that you need to use your mentorchains email to access it.


Don't worry if you haven't started yet! The self-assessment isn't due until tomorrow. As such, we'll get everyone on the same page starting early next week.

If you are having difficulty with any of these initial steps, please join our Office Hours today, Friday 17 at 10am PDT at this link: https://meet.google.com/syg-gyoh-esw
Mentors, Leads and Technical Trainers will be online to answer your queries and give you a helping hand!

Hi, I just downloaded all the data, and read it into R with the ReadAffy function. How do I merge the two data sets?

Hi @asrira428, I believe you can just use the merge function:

merge(data1, data2)

where data1 and data2 are the objects from ReadAffy

Hi, I have been trying to use the arrayQualityMetrics function, but an error occurs stating that the program “cannot allocate vector of size ____.” Is this a computer memmory issue?

Yeah, it’s a memory issue. You can allocate more memory using the function

memory.limit(arg)

where arg is the amount of memory you want to allocate. The documentation says arg is in Mb but you have to allocate more than what it says in the error.

Thank you for the advice. I tried using memory.limit(arg) earlier, but it said that I “cannot decrease memory limit.” I ended up restarting my computer and then ran the program again. There was a long wait, but I was able to generate the report.

Update: When viewing the .html file, the report ended at Section 3: Variance mean dependence. Does this mean that the generation was incomplete?

Probably, do you have RLE and NUSE plots in the folder?

I tried running memory.limit again and used

memory.limit(size=1000000)

as the arg (a bit of an overkill). I think everything generated this time. Thank you.

Great!