small dimensions in the matrix of counts from smallRNA using DESEq2
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andreia • 0
@andreia-23745
Last seen 7 days ago
Portugal

Hi there,

I am doing smallRNA data analysis and I have a matrix of counts 17 miRNA and 16 samples I wonder if its correct to perform the results() from DESeq2 to get the DEM's.

Is there a minimum number of miRNA that is correct to perform the analysis with DESEq2 package?

Please, can anyone help me about this doubt?

Thanks in advance

Andreia

matrix DESeq2 SmallRNA dimensions small • 242 views
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What kind of assay is this? With only 17 miRNAs it is probably not NGS, is it? What are the values, are these counts?

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Yes they are raw counts.

I know that is very small data! I did in past 2 data smallRNAseq analysis (not alot experience but i have a steady workflow...) but nothing with this quality. I already told the client about this.

This is from semen samples and the wetlab protocol is hard to get a good quality and quatity of RNA... :/

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And yes is NGS :)

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@mikelove
Last seen 1 hour ago
United States

With 17 features, I would first doubt the accuracy of the size factors. The dispersion estimates will be decent because of the 16 samples, but if you don't know what is "housekeeping" then there's no hope for DE analysis with so few features.

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What method do you recommend to use in this type of dimensions data smallrna for differential expression?

Thanks

Andreia

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I don't have any suggestions here, I'd be worried how to normalize the data.

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I tested TMM and quantile normalization like some papers about smallRNA tested, actually i think there is no THE BEST normalization method :/ for this type of the analysis, the same thing with the aligner (i tested bwa and bowtie for this dataset with similar results).

In my particular case its harder, the data that came out its not helping i'm afraid.

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