raw data normalization

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2.8 years ago

Nobody ▴ 30

Hi!

I have raw public data from the SRA database (fastq format), I would like to evaluate the batch effect and normalize my data. Is it possible to normalize them ? how ?. what are the programs in R that will allow me to make a correction of the batch effect. Finally, I would like to know the pre-processing to be done before proceeding to the alignment and the assembly of my data.

I appreciate all suggestions.

Thank you

rna-seq • 751 views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 2.8 years ago by Nobody ▴ 30

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We don't know what your data is or what the goal of your analysis is. You should expand on your project and hypothesis otherwise it would be difficult for us to help.

ADD REPLY • link 2.8 years ago by rpolicastro 13k

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What RNASeq tutorial are you following? You are about 5 steps away from being able to assess batch effect. If your hope is to compare samples from two totally different labs, that's likely to be impossible.

ADD REPLY • link 2.8 years ago by swbarnes2 14k

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