mRNA expression, RSEM( Batch normalized from illumina Hiseq_RNAseq)

[dan jin]

Hi cBioPortal support group,

I am trying to get the top expressed chemokine genes from GBM samples. Can I directly use the mRNA expression, RSEM( Batch normalized from illumina Hiseq_RNAseq) data in download for analysis? Do I need to do other normalization?

Thanks,

Dan

[Benjamin Gross]

Hi Dan,

I’m not sure what type of analysis you are performing, but when it comes to gene expression analysis, you want to avoid comparing across cohorts to minimize issues associated with batch effects. However, you can use the data directly when comparing within a cohort. Of course, expression should also be interpreted relative to some baseline value. For example, we provide z-scores relative to diploid (CNA) samples within the cohort or relative to all samples.

Best,

-Benjamin

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cbioportal/8c01ecca-1245-4adf-ac4a-9e3c0372f5e5n%40googlegroups.com.

[dan jin]

Hi Benjamin,

I’m comparing gene expression within cohort ( for example , comparing ccl2 with ccl8 in the same patient). To reduce the variation among different patients data from batch effect , would you recommend using the Z score to diploid sample or all samples? Or do you have other better options?

Thanks!

Dan

[Benjamin Gross]

Hi Dan,

I’m an engineer on the cBioPortal team, not an analyst, so I recommend you get advice from an active researcher (there are researchers following this forum and may have some advice).  The trade-off between using diploid vs all samples is that, in the former case, you are only considering samples that are not over- or under-expressing from a CNA perspective. Of course, the sample size is probably smaller.  There may be other nuances, that, as an engineer, I’m not aware of. 

I hope this helps.

Best,

-Benjamin

[dan jin]

Thank you Benjamin! I will wait to see if anyone else in the group could provide some advice.  

Best 

Dan