User: Steve

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Steve10
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Posts by Steve

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Comment: C: Affymetrix Power Tools Error #2
... 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 ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error #2
... 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 ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error #2
... 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? ...
written 3.3 years ago by Steve10
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Affymetrix Power Tools Error #2
... 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.8Nv ...
software error rma microarray error apt written 3.3 years ago by Steve10 • updated 3.3 years ago by genomax75k
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Comment: C: Affymetrix Power Tools Error
... 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 t ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error
... 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 ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error
... 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.CE ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error
... When I did that, it gave me this error -> FATAL ERROR:Can't read file: 'GSM538415_EA07068_52753_MoGene_T.8Nve_Sp_1.CEL' ...
written 3.3 years ago by Steve10
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Comment: C: Affymetrix Power Tools Error
... 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. ...
written 3.3 years ago by Steve10
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Affymetrix Power Tools Error
... 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 ma ...
gene software error microarray cel files apt written 3.3 years ago by Steve10 • updated 3.3 years ago by WouterDeCoster42k

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