Problems with Edge R normalization in same sample but using different ref genomes.

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salvocomplicazioni1 • 0

@salvocomplicazioni1-14125

Last seen 10 months ago

Germany

Hi

Starting from Rna-seq data raw counts, I used TCGAanalyze_Normalization function based on edger, so i obtained normalized count. If i perform same analysis on two data type (GRCh37 and GRCh38) i obtain completely different normalized counts.

Results are these:

GRCh38

	Sample1
GLI1	27436
ST3GAL1	0
SOX2	2

GRCH37

	Sample1
GLI1	451
ST3GAL1	9583
SOX2	5

If i look at two bam file (aligned against 37 ad aligned against 38), they showed the exactly amount of reads for each mentioned genes, so i think that problem is on normalization?

What are the differences?

Thanks in advance.

normalized counts grch37 grch38 r bioconductor • 1.0k views

ADD COMMENT • link 6.6 years ago salvocomplicazioni1 • 0

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You have given just enough information for people to know that you did some stuff and you got some numbers. Unless you say exactly what you did, how could anybody help you?

ADD REPLY • link 6.6 years ago James W. MacDonald 65k

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