Entering edit mode
7.7 years ago
Steve
▴
10
I have been trying to filter microarray data by using affymetrix power tools. I have been coming across obstacles and now I have an error for reading the cdf. My input was ->
apt-probeset-summarize -a rma -d MoGene-1_0-st-v1.r3.cdf -o output /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve.Sp_1.CEL
And it gives me the error ->
FATAL ERROR:EngineUtil::getCdfChipType() - Can't read header for 'MoGene-1_0-st-v1.r3.cdf'. Description: Unable to open the file.
What does this mean? Would anyone be able to help me?
This appears to be a similar problem like the one in your last post. You need to provide the full path to the cdf file and make sure it is readable by everyone by doing a
chmod a+r MoGene-1_0-st-v1.r3.cdf.I am going to echo @Wouter and say that it would help you immensely if you spend half a day learning the basics of unix command line here.
When I do -> chmod a+r MoGene-1_0-st-v1.r3.cdf
Output is -> chmod: cannot access 'MoGene-1_0-st-v1.r3.cdf': No such file or directory
I want to ask, if I am running Linux ubuntu off a live usb, would that have any effect to why it doesnt want to read?
You need to issue that command in the directory where that file is present or provide full path to the file if it is in another directory.
Glad you mentioned that you are using ubuntu off live USB. That is probably not a good way of trying to do this analysis. It may be better if you use a virtual machine (I assume you are on windows?).
When I type in the full path to the file and run the chmod a+r command, it gives me no output. It just goes to a new line. Is this what I should be expecting when I type in the command
what does
ls -lh /path_to/MoGene-1_0-st-v1.r3.cdfshow?It says -> cannot access: (path to file): No such file in directory
I will say this, I have used this file in another computer and it has seemed to recognize it. Unfortunately, APT software does not run on the OS of the mac I have. Now I am beginning to think that it is because I am running off a live usb for ubuntu.
APT installer for Mac says "yosemite". What OS X are you using? I assume you have already tried to use the binary provided? Did that not work?
If you are brave you can always download the source and try to compile the program yourself (but do that only if the above does not work).