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 am using Affymetrix Power tools to filter the data. I tried to follow the instructions on the manual but when I input in the command ->
- apt-probeset-summarize -a rma -d MoGene-1.0-st-v1.r3.unsupported-cdf -o GSM538415_EA07068_52753_MoGene_T.8Nve.Sp_#1.CEL
I receive an error message saying -> FATAL ERROR:No cel files specified.
Has anyone come across this problem or does anyone know how I may be able to fix it?
Yes, GSM538415_EA07068_52753_MoGene_T.8Nve.Sp_#1.CEL is the cel file. I am not quite understanding what the output directory would be. I have the file located in the Home directory in a folder called APT.
It is possible that the # sign in the name of the CEL file are messing things up. Can you rename the file and try again?
It also appears that you need to explicitly provide an output directory name (based on @Wouter's find above, I have renamed the CEL file to remove the special characters).
You also appear to be missing additional files (or command line directives) based on the example above, which may be needed for this to work.
When I did that, it gave me this error -> FATAL ERROR:Can't read file: 'GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL'
Where is the CEL file located? If it is in APT directory then you need to provide full path to it. If I recollect your other post then that path would be /APT/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL so try (replace new_output_dir with the name of an appropriate directory)
I looked up the path to the cel file and it gave me -> /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL
From there I did the input -> apt-probeset-summarize -a rma -d MoGene-1.0-st-v1.r3.unsupported-cdf -o new_output_dir /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL
And I have the error: Cant read file: /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL
Can't read filecould be because of two reasons.
Can you check on possibility #2?
ls -lh /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CELshow a non-zero byte size?
When I did that command it gave me this -> ls: cannot access /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL : no such file or directory
I also tried the chmod command and it gave me the same output. ->cannot access /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL
I tried the new command that you suggested but it still says it no cel files specified.
Also because I am running ubuntu from a live usb, would that have any detrimental affect to what I want to do?
That is odd. Are you certain the file is indeed in that directory? Is
Can you try doing
chmod a+x /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL? (you may need to add
sudoat the beginning and provide an admin password if you are not able to complete the command).
WouterDeCoster why do you say that the syntax would be ->
usage: apt-probeset-summarize -a rma-sketch -a plier-mm-sketch \ -p chip.pgf -c chip.clf -o output-dir *.cel
When I read it shows in the manual that ->
On unix systems a command to do both rma-sketch and plier-sketch analysis at the same time with the default parameters looks like:
apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d chip.cdf -o output-dir *.cel
If that is the command you want to use then try it exactly that way. You only had
-a rmain your original post.