lineage analysis read error reading EnsMart65 Rn_3 something

[Hazard, E. Starr]

Nathan,

(AA 2.0.7 MAC 64 bit) Working with Rat data.

I am trying to run Lineage Analysis and I get an errno 2 No such file or directory

Applciations/AltAnalyze/AltDatabase ENSMART65/ensembl/Rn/Rn_3....

I cannot read the final bit.

Is there a log produced for interactive running of Lineage Profiler?


I have a bunch of files labelled Rn_Ensembl_ in my /AltAnalyze/AltDatabase ENSMART65/ensembl/Rn directory

Is the script forced to look to for some thing with Rn_3.... ??


http://useast.ensembl.org/multi/martview

gives a 404 error

Thanks
Starr

[Nathan Salomonis]

Hi Starr,

This is probably not spelled out everywhere that well, but as of right
now LineageProfiler only works for mouse and human. This won't be the
case in the next version and will work for rat based on inference. If
you want to do this now, you will need to convert your gene expression
set (exp.YourDataset-steady-state.txt) from rat to mouse ensembl gene
IDs and then analyze as mouse.

You can however still use related functionality for rat when doing the
pathway enrichment analyses through AltAnalyze by selecting the
Biomarker gene set option which includes these LineageProfiler marker
predictions. In fact, for finding differences in cellular composition
between groups, this function is more sensitive than the above
methods.

Best,
Nathan

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