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Old 03-02-2011, 03:22 PM   #1
Adam Witney
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Location: London

Join Date: Mar 2011
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Default myrna generates all p-values = 1.000000e+00

I am trying to get myrna working on our bacterial RNA-seq data.

I first modified a reftools shell script to access EnsemblBacteria for the Streptococcus genome and this seems to work ok.

After running myrna all the directories and files seem to be created but all genes have a p-value of 1.000000e+00 in the pvals.txt file.

The dataset has no replicates so only has one fastq for each of 2 conditions, but I wouldn't expect all p-values to be exactly 1. Do i need more replicates or is something not running correctly within the process?

thanks

adam
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Old 03-02-2011, 05:40 PM   #2
Ben Langmead
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Hi Adam,

Can you send me the log of your run? (Myrna prints out a message at the end indicating what the output-dump file is named.) Also, can you send me the count_table.txt file from the run?

Thanks,
Ben

Quote:
Originally Posted by Adam Witney View Post
I am trying to get myrna working on our bacterial RNA-seq data.

I first modified a reftools shell script to access EnsemblBacteria for the Streptococcus genome and this seems to work ok.

After running myrna all the directories and files seem to be created but all genes have a p-value of 1.000000e+00 in the pvals.txt file.

The dataset has no replicates so only has one fastq for each of 2 conditions, but I wouldn't expect all p-values to be exactly 1. Do i need more replicates or is something not running correctly within the process?

thanks

adam
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Old 03-16-2011, 12:05 AM   #3
Rachelly
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Location: Israel

Join Date: Oct 2010
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Hi,

I'm facing a similar problem, but I get all the p-values as 0.000000e+00, which is also unlikely..
Any conclusions on this issue?

Thanks,
Rachelly.
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Old 03-28-2011, 07:47 AM   #4
Adam Witney
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Location: London

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In my case the p-value's of 1.000000e+00 were being generated as there were no replicates in this dataset.

I don't know enough about the system to answer your question, but maybe Ben can help you.

Adam
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Old 10-20-2011, 11:39 AM   #5
csmatyi
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Same problem for us over here! All of our p-values come out as 1.
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