Inconsistent gene ordering in pbta-gene-expression-rsem-fpkm.stranded.rds

[jashapiro]

What data file(s) does this issue pertain to?

pbta-gene-expression-rsem-fpkm.stranded.rds

What release are you using?

v12

Put a link to the relevant section of the [OpenPBTA-manuscript]

Put your question or report your issue here.

The gene order in file pbta-gene-expression-rsem-fpkm.stranded.rds does not match the other rsem data files. In particular the following gene_ids are not in the same positions between files.

> cbind(fpkm_rsem_polyA$gene_id, fpkm_rsem_stranded$gene_id)[fpkm_rsem_polyA$gene_id!=fpkm_rsem_stranded$gene_id,]
      [,1]                                [,2]                               
 [1,] "ENSG00000124333.15_PAR_Y_VAMP7"    "ENSG00000124333.15_VAMP7"         
 [2,] "ENSG00000124333.15_VAMP7"          "ENSG00000124333.15_PAR_Y_VAMP7"   
 [3,] "ENSG00000167393.17_PAR_Y_PPP2R3B"  "ENSG00000167393.17_PPP2R3B"       
 [4,] "ENSG00000167393.17_PPP2R3B"        "ENSG00000167393.17_PAR_Y_PPP2R3B" 
 [5,] "ENSG00000168939.11_PAR_Y_SPRY3"    "ENSG00000168939.11_SPRY3"         
 [6,] "ENSG00000168939.11_SPRY3"          "ENSG00000168939.11_PAR_Y_SPRY3"   
 [7,] "ENSG00000169100.13_PAR_Y_SLC25A6"  "ENSG00000169100.13_SLC25A6"       
 [8,] "ENSG00000169100.13_SLC25A6"        "ENSG00000169100.13_PAR_Y_SLC25A6" 
 [9,] "ENSG00000182378.13_PAR_Y_PLCXD1"   "ENSG00000182378.13_PLCXD1"        
[10,] "ENSG00000182378.13_PLCXD1"         "ENSG00000182378.13_PAR_Y_PLCXD1"  
[11,] "ENSG00000182484.15_PAR_Y_WASH6P"   "ENSG00000182484.15_WASH6P"        
[12,] "ENSG00000182484.15_WASH6P"         "ENSG00000182484.15_PAR_Y_WASH6P"  
[13,] "ENSG00000185203.12_PAR_Y_WASIR1"   "ENSG00000185203.12_WASIR1"        
[14,] "ENSG00000185203.12_WASIR1"         "ENSG00000185203.12_PAR_Y_WASIR1"  
[15,] "ENSG00000185960.13_PAR_Y_SHOX"     "ENSG00000185960.13_SHOX"          
[16,] "ENSG00000185960.13_SHOX"           "ENSG00000185960.13_PAR_Y_SHOX"    
[17,] "ENSG00000214717.11_PAR_Y_ZBED1"    "ENSG00000214717.11_ZBED1"         
[18,] "ENSG00000214717.11_ZBED1"          "ENSG00000214717.11_PAR_Y_ZBED1"   
[19,] "ENSG00000223274.6_PAR_Y_RNA5SP498" "ENSG00000223274.6_RNA5SP498"      
[20,] "ENSG00000223274.6_RNA5SP498"       "ENSG00000223274.6_PAR_Y_RNA5SP498"
[21,] "ENSG00000223484.7_PAR_Y_TRPC6P"    "ENSG00000223484.7_TRPC6P"         
[22,] "ENSG00000223484.7_TRPC6P"          "ENSG00000223484.7_PAR_Y_TRPC6P"   
[23,] "ENSG00000225661.7_PAR_Y_RPL14P5"   "ENSG00000225661.7_RPL14P5"        
[24,] "ENSG00000225661.7_RPL14P5"         "ENSG00000225661.7_PAR_Y_RPL14P5"  

[kgaonkar6]

Sorry I just checked ,the inconsistency arise because of the way I merged the gene fpkm files.

I used tximport https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html (rsem mode) to merge the all (new and existing) stranded rsem gene FPKM files while rsem polya FPKM files were merged by @tkoganti using this script https://github.com/kgaonkar6/OpenPBTA-analysis/blob/master/analyses/collapse-rnaseq/00-create-rsem-files.R.

I'll redo the merging using the same script which will make it consistent with the other rsem files.

[jaclyn-taroni]

Looking at the v13:

> identical(`pbta-gene-expression-rsem-fpkm.polya`$gene_id, `pbta-gene-expression-rsem-fpkm.stranded`$gene_id)
[1] TRUE

Closing this issue.