Question: Is it possible to analyze together rna seq outputs from cufflinks and rsem?
gravatar for SandraGarcia
3.1 years ago by
Barcelona, Spain
SandraGarcia10 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 • 1.1k views
ADD COMMENTlink modified 3.1 years ago by Kevin Blighe67k • written 3.1 years ago by SandraGarcia10
gravatar for Kevin Blighe
3.1 years ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Edit: answer updated February 4th, 2019

You're implying that you want to merge the datasets together? There may be no precedent for merging FPKM and RSEM v2 counts. If I were forced to do it, I would process the RSEM counts independently via tximport/DESeq2 and ultimately produce variance-stabilised counts, which I would then transform to Z-scale. I would then also convert the FPKM counts to Z-scale via zFPKM (R package). On the Z-scale, the distributions are at least comparable. You would likely have to include, as a covariate, SOURCE (FPKM or RSEM) in all downstream modeling from that point forward.

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

Hope this helps!


ADD COMMENTlink modified 21 months ago • written 3.1 years ago by Kevin Blighe67k

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 3.1 years ago by SandraGarcia10


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.

ADD REPLYlink modified 21 months ago • written 3.1 years ago by Kevin Blighe67k
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