Errors in Gene Expression Data for Daniel's Landscape Paper

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Errors in Gene Expression Data for Daniel's Landscape Paper #46

Closed khanjav closed 6 months ago

khanjav commented 7 months ago

Hsien-chao, the TPM expression level of various genes, such as PHOX2B and MYCN is wrong in the data generated by @abidgen. Can you work with Abid and Jun to figure out where the error occurred?

hsienchao commented 6 months ago

I used another tool called gffcompare to map the stringTie transcripts to gencode annotation. The results of Pearson correlation for each gene are attached. Overall the protein coding genes have higher correlation (mean 0.926). Level 1 coding genes (validated) is 0.95. LncRNA has poor mean correlation (0.72). I’ve copied the new count/tpm/length to Box\lncRNA_Landscape\StringTie\updated.

Below is the correlation of some genes of interests.