Question: kal's test on rpkm vs raw counts
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gravatar for from the mountains
9 weeks ago by
United States
from the mountains40 wrote:

For comparisons with 0 replicates, I am using Kal's Z-test on proportions. I am wondering, does it make more sense to run Kal's on RPKM or on raw counts, and why? I would think that RPKM is better because it is normalized by gene length. We are more interested in knowing the (transcripts_of_geneA/total_transcripts) rather than (reads_of_geneA/total_reads), aren't we? I can see however that they can yield slightly different results in some cases.

I see conflicting information on each alternative. On the one hand, the Kal's paper writes the equation as (n-specific mRNA reads/cell)/(N-total mRNA reads/cell), but on the other hand, when I try to run the function on RPKM in CLC it warns me that proportions tests are aimed at count data.

Which is better?

rna-seq • 177 views
ADD COMMENTlink modified 9 weeks ago by theobroma221.0k • written 9 weeks ago by from the mountains40

Could you elaborate on what it is you actually want to do? Then we migth be better able to help you.

ADD REPLYlink written 9 weeks ago by kristoffer.vittingseerup350
0
gravatar for theobroma22
9 weeks ago by
theobroma221.0k
theobroma221.0k wrote:

CLC Bio is a licensed platform, so it may be best for you to contact CLC to get an answer to your question. However, Karl's test is for the count data and not RPKM.

ADD COMMENTlink written 9 weeks ago by theobroma221.0k

good to know. but why? and doesn't that seem in conflict with the formula stated in the kal's test paper? : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC25383/

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by from the mountains40

Not at all. You have to consider the experimental design of SAGE vs. RNA-seq, which is what you used.

ADD REPLYlink written 9 weeks ago by theobroma221.0k
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