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Question: cuffdiff-quartile normalization method
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gravatar for raj_262920
3.8 years ago by
raj_262920 • 20
Germany
raj_262920 • 20 wrote:

Hello

Why does the quartile normalization method does not produce any FPKM values for my data with the reference genome ( and 'NOTEST' for all the values) whereas geometric method produce many FPKM values and identifies significance?

What does that mean ? What is the difference and is it really significant ?

Thanks
rna-seq galaxy • 1.9k views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by raj_262920 • 20
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The "NOTEST" result from Cuffdiff indicates that there was not enough data to perform the calculation. It could be that your data is shallow? Double check the mapping rates/jobs if this does not seem to be a good explanation for your particular inputs/reference genome and annotation.

Not infrequently, poor mapping rates can be traced all the way back to the quality score scaling of the input fastq data. If you wish to double check your fastq data, this wiki can help show you how:
http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

For more detail, "NOTEST" is defined here in the manual:
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#differential-expression-tests

For help in understanding the different "Library Normalization" (–library-norm-method) methods, please see the descriptions at:
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cuffdiff-options -> http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#library-normalization-methods

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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