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NCI60 RNA data misannotated #59

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p-smirnov opened this issue May 3, 2023 · 0 comments
Open

NCI60 RNA data misannotated #59

p-smirnov opened this issue May 3, 2023 · 0 comments

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@p-smirnov
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I am not sure what happened in the creation of the NCI60 PSet, but the feature into of the RNASeq data is completely misaligned with the row names of the object. For example:

> rowData(molecularProfiles(NCI60)$rnaseq.comp["ERBB2",])
DataFrame with 1 row and 9 columns
              gene_id hugo_symbol entrez_gid    cytoband          gene_name_url
          <character> <character>  <numeric> <character>            <character>
ERBB2 ENSG00000203663       OR2L2      26246        1q44 http://www.genenames..
              entrez_gid_url      genomic_coord_url       gene_description
                 <character>            <character>            <character>
ERBB2 http://www.ncbi.nlm... https://www.ncbi.nlm.. olfactory receptor f..
                 ensembl_tid
                 <character>
ERBB2 ENST00000642011|ENST..
> rowData(molecularProfiles(NCI60)$rnaseq.iso["ERBB2",])
DataFrame with 1 row and 9 columns
              gene_id hugo_symbol entrez_gid    cytoband          gene_name_url
          <character> <character>  <numeric> <character>            <character>
ERBB2 ENSG00000203663       OR2L2      26246        1q44 http://www.genenames..
              entrez_gid_url      genomic_coord_url       gene_description
                 <character>            <character>            <character>
ERBB2 http://www.ncbi.nlm... https://www.ncbi.nlm.. olfactory receptor f..
                 ensembl_tid
                 <character>
ERBB2 ENST00000642011|ENST..

The PSet needs to be fixed.

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