Affymetrix Power Tools

Question

[Steve]

Hello All,

I have raw microarray data that comes as .cel files. Before I start analysis, I need to filter the data (background adjustment, quantile normalization, median polish probeset summarization) I came across Affymetrix Power Tools which should be proper to help me accomplish my goals. However, I am not command line savy and the instructions they give on how to use APT are a bit confusing to me. I am running a 64bit Linux Ubuntu OS on my laptop and my questions are:

1. Is it possible to run this software off of my laptop?
2. If so, then would someone be able to point me in the right direction on how to install and use?
3. If my laptop does not meet the APT standards is there another option on accomplishing my goal?

[WouterDeCoster]

You haven't approved an answer in your two previous questions, it would be appropriate if you do so if any answer was satisfactory. (General remark, not just because I tried answering them.)

That said, did you download the software? Did you read a manual? I would guess that an average laptop should be able to handle it (unless it's a prehistoric one but you haven't specified anything about it's memory or computing power.)

[Steve]

My apologies WouterDeCoster. Yes, they were more than satisfactory and very insightful. I have downloaded the newest version of the APT software and extracted the files. But after that, the process becomes a bit overwhelming for me. It prompts me to copy the files to a dir on your $PATH or add the bin directory to your path. This is the first problem that I have come across. I have searched how to do this but I still am not comprehending the process.

[WouterDeCoster]

When you want to execute a program, your operating system needs to know where it is localized. It will search in the directories in $PATH. You can check what's in your $PATH by executing echo $PATH in a terminal window.

So you have to either change the $PATH or make sure that your files are in a directory listed in $PATH. To change the $PATH, you can - Temporarily add a directory by using export PATH=$PATH:/path/to/files/you/installed/bin (note that a : is used as separator!) - Permanent change the PATH as how it is specified in your ~/.bashr file (hidden file in your home directory)

To put the files in a directory listed in $PATH you can either copy them to a directory like that or create symbolic links so that would be cp /path/to/files/you/installed/bin/* /a/certain/path/listed/in/$path or ln -s /path/to/files/you/installed/bin/* /a/certain/path/listed/in/$path

I would recommend to create symbolic (soft)links to a personal bin directory in the home directory.

[Steve]

Thank you for your help WouterDeCoster. So I tried the recommended procedure and I was unsuccessful. I went to the terminal. Then my steps were.

1. echo $PATH -> (Gave me the result of) /home/ubuntu/bin:/home/ubuntu/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
2. export PATH=$PATH:/APT (APT is the folder with the downloaded files in my home folder) 3.(When I do, echo $PATH, it gave me this output ->) /home/ubuntu/bin:/home/ubuntu/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/APT
3. (Then to check I ran the command ->) apt-probeset-summarize
4. (Which gave me this output ->) apt-probeset-summarize: command not found

[GenoMax]

There must be a bin directory under APT (if it is not directly there then figure out where it is) where apt-probeset-summarize lives. If that is the case the you need to add /APT/bin to your $PATH. Then try re-running apt-probeset-summarize command.

[WouterDeCoster]

Aw you beat me by a few seconds :-0 but you have a different hypothesis to what's wrong. Also possible :p

[WouterDeCoster]

As a side note I would advice you to follow some command line tutorials, e.g. https://www.codecademy.com/learn/learn-the-command-line

Those could help you to understand what's going on and what's going wrong.

You almost did the procedure correctly. However, you told your operating system that there are programs in /APT, but that directory doesn't exist as such. You need to define the complete path (aka absolute path). When you are in the directory above APT you should run readlink -f APT which will show you the full path. The path starts from the root directory / and will most likely be something like /home/ubuntu/APT or a variation to that.

You can't just tell the operating system in which directory the tools are without giving a complete address. The mailman wouldn't find a house if the letter didn't contain also the city and country.

Is that clear?

These are really basic elements of Unix/Linux and command line usage, so you'll do things like this for the rest of your bioinformatics career. Better to study a bit now and have profit from that forever. Good luck!

[Steve]

Thank you for the resources and help WouterDeCoster. I really appreciate your time and patience with my questions. I will most certainly look into the command line tutorial and hope to polish my skills in that area.