HI,
I want to compare my RNA-seq with microarray which is found on GEO to indicate the highly correlation between them. I search many papers but found little information about details of comparing RNA-seq and microarray.
there is my workflow
1. mapping probe seq to refseq to cluster refseq to certain probeset. such as probeset A can be mapped to refseq A and B.
2. calculate reads mapping on these refseq and if one reads can be mapped to both A and B, it is counted only once.
3. calculate pearson corlation using microarray probeset intesity and RNA-seq reads counts.
can you tell me where can I improve? for the correlation between my RNA-seq and microarray is not very good (pearson corelation=0.589)
Thanks
I want to compare my RNA-seq with microarray which is found on GEO to indicate the highly correlation between them. I search many papers but found little information about details of comparing RNA-seq and microarray.
there is my workflow
1. mapping probe seq to refseq to cluster refseq to certain probeset. such as probeset A can be mapped to refseq A and B.
2. calculate reads mapping on these refseq and if one reads can be mapped to both A and B, it is counted only once.
3. calculate pearson corlation using microarray probeset intesity and RNA-seq reads counts.
can you tell me where can I improve? for the correlation between my RNA-seq and microarray is not very good (pearson corelation=0.589)
Thanks
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