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Old 11-05-2014, 11:31 AM   #1
surjray
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Location: Florida

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Default Empty log2fold change rows in DEXSeq

Dear all,
I have been analyzing some Drosophila data through DEXSeq and have found that in the final results table, several rows have empty log2fold values. These exons however do have P values and adjusted P values. I am using the estimateExonFoldChanges command to estimate fold changes. I am not sure if this is because of the minCount or maxExon restrictions.
I am using the latest version of DEXSeq.
Thanking you.
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Old 11-07-2014, 11:12 PM   #2
Wolfgang Huber
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Dear Surjray

it may be difficult to help you based on the information provided. Can you post a self-contained code example (with example data, e.g. you could use the 'pasilla' package) that reproduces your problem. Also the output of 'sessionInfo()'.

To exclude the trivial, it looks like your screenshot is from a spreadsheet software, and these do not always behave as intended when importing data from text files such as produced by DEXSeq. Can you double-check how the output from DEXSeq looks in a text editor (like Notepad).

Wolfgang
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