Question: Is it possible to analyze together rna seq outputs from cufflinks and rsem?
gravatar for SandraGarcia
9 months ago by
Barcelona, Spain
SandraGarcia0 wrote:

Hello everyone! I want to analyze together the gene expression profiles from two different datasets and compare a number of genes between the two. One of them is in rsem v2 output format, and the other in fpkm (cufflink output). I have triend calculating the fpkm from rsem raw counts, but the distributions do not correlate at all so I am not sure if it would be possible to compare the gene expression among them as the data do not seem to be in the same scale.

Do you have any idea if it is possible to make these two data type comparable?

Thank you in advance,


rsem rna-seq cufflinks fpkm • 364 views
ADD COMMENTlink modified 9 months ago by Kevin Blighe23k • written 9 months ago by SandraGarcia0
gravatar for Kevin Blighe
9 months ago by
Kevin Blighe23k
Republic of Ireland
Kevin Blighe23k wrote:

You're implying that you want to merge the datasets together? I think that the best approach would be to convert both datasets independently to the Z-scale and to then see how they line up in a histogram (and also do your correlation analyses). Another option could be to use one dataset as the training dataset, and the other as the validation dataset.

If you go down the merging route, then you will always be criticised by reviewers when trying to publish.

Hope this helps!


ADD COMMENTlink written 9 months ago by Kevin Blighe23k

Thank you Kevin, I will go for it. Yes I want to merge the two datasets. We are also thinking of asking for the permissions to have the bam files of the second dataset so I will be able to re-analyze them with the same software.

ADD REPLYlink written 9 months ago by SandraGarcia0


Well, the BAM files would help, but they would still be produced very differently, i.e., a BAM produced by Bowtie/TopHat is very different from a BAM produced by some other aligner. You will just have to be very methodical when merging these datasets. I mentioned Z-scores because I had success with that in the past, but the differences between RSEM and FPKM are even great than the differences that I encountered.

ADD REPLYlink written 9 months ago by Kevin Blighe23k
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