Affymetrix Power Tools Error
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7.8 years ago
Steve ▴ 10

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 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?

software-error CEL APT Microarray gene • 3.1k views
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7.8 years ago

The error message is really clear in what the problem is. The program needs cel files specified at the end of the command

Based on http://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html, synthax should be like:

usage: apt-probeset-summarize -a rma-sketch -a plier-mm-sketch \ -p chip.pgf -c chip.clf -o output-dir *.cel

I assume your cel file is GSM538415_EA07068_52753_MoGene_T.8Nve.Sp_#1.CEL? You have to provide an argument for the -o flag: the output directory

Most commandline tools have buildin help... I would guess apt-probeset-summarize --help could tell you something

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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.

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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).

apt-probeset-summarize -a rma -d MoGene-1.0-st-v1.r3.unsupported-cdf -o  new_output_dir  GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL

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.

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When I did that, it gave me this error -> FATAL ERROR:Can't read file: 'GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL'

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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)

apt-probeset-summarize -a rma -d MoGene-1.0-st-v1.r3.unsupported-cdf -o  new_output_dir  /APT/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL
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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

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Can't read file could be because of two reasons.

  1. You don't have read permissions (unlikely since it seems to be in your home directory).
  2. The file is empty or corrupt

Can you check on possibility #2?
Does ls -lh /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL show a non-zero byte size?

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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?

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That is odd. Are you certain the file is indeed in that directory? Is ubuntu your username?

Can you try doing chmod a+x /home/ubuntu/GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL? (you may need to add sudo at the beginning and provide an admin password if you are not able to complete the command).

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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

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If that is the command you want to use then try it exactly that way. You only had -a rma in your original post.

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