Inconsistant table in pbta-gene-counts-rsem-expected_count.stranded.rds

[jashapiro]

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

pbta-gene-counts-rsem-expected_count.stranded.rds
less so:
pbta-gene-expression-rsem-tpm.stranded.rds

What release are you using?

v12

Put your question or report your issue here.

The count table in pbta-gene-counts-rsem-expected_count.stranded.rds has an extra column at the start of the data table, labeled X which contains only 0 indexed row numbers. This does not appear in
pbta-gene-counts-rsem-expected_count.polyA.rds This column should presumably be removed in future versions.

Additionally, the gene_id column in pbta-gene-counts-rsem-expected_count.stranded.rds and pbta-gene-expression-rsem-tpm.stranded.rds is stored as factor, not as character, in contrast to all other files.

[jharenza]

cc-ing @tkoganti, who can fix this in V13

[tkoganti]

Fixed pbta-gene-counts-rsem-expected_count.stranded.rds file and uploaded file to V13-data

[tkoganti]

Both the files are uploaded under V13-data here - https://cavatica.sbgenomics.com/u/cavatica/pbta/files/#q?path=processed-data-merge%2FV13-data

[tkoganti]

@jharenza I checked that both the files have samples within the pbta-histologies file.
pbta-gene-expression-rsem-tpm.stranded.rds was okay
pbta-gene-counts-rsem-expected_count.stranded.rds file had one extra sample BS_4X8PQ5G6 that I deleted and uploaded the updated file here - https://cavatica.sbgenomics.com/u/cavatica/pbta/files/5e1d165fe4b09d9aaf49571b/

[jaclyn-taroni]

Looking at pbta-gene-counts-rsem-expected_count.stranded.rds in v13:

> `pbta-gene-counts-rsem-expected_count.stranded`[1:5, 1:5]
                      gene_id BS_014EVM2D BS_02NZT8CE BS_03FT4S8B
1   ENSG00000000003.14_TSPAN6        2273        1531        5005
2      ENSG00000000005.5_TNMD           3          10          10
3     ENSG00000000419.12_DPM1         674         555        2282
4    ENSG00000000457.13_SCYL3         771         758        1962
5 ENSG00000000460.16_C1orf112         360         522         677
  BS_0448A413
1        1317
2          12
3         569
4         534
5         355


> head(sapply(`pbta-gene-counts-rsem-expected_count.stranded`, class))
    gene_id BS_014EVM2D BS_02NZT8CE BS_03FT4S8B BS_0448A413 BS_044XZ8ST 
"character"   "numeric"   "numeric"   "numeric"   "numeric"   "numeric" 

and pbta-gene-expression-rsem-tpm.stranded.rds in v13:

> head(sapply(`pbta-gene-expression-rsem-tpm.stranded`, class))
    gene_id BS_014EVM2D BS_02NZT8CE BS_03FT4S8B BS_0448A413 BS_044XZ8ST 
"character"   "numeric"   "numeric"   "numeric"   "numeric"   "numeric" 

Closing this issue.