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Update 1_convert-tpm-hugo.ipynb #1

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6 changes: 3 additions & 3 deletions care/1_convert-tpm-hugo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"\n",
"Changelog:\n",
"2018-05-02 : Sum the TMP values, rather than take the mean, of combined duplicate genes See issue #130.\n",
"2017-12-05 : Average genes together in TPM space, not log2 TPM space; the latter is incorrect.\n",
"2017-12-05 : Average genes together in TPM space, not log2 TPM space; the latter is incorrect. (later changed to summing genes)\n",
"\n",
"Input : \n",
" - conf.json\n",
Expand All @@ -40,7 +40,7 @@
"- TPM column extracted\n",
"- ensembl genes translated to hugo\n",
" - File written as rsem.genes.tpm.hugo.tab\n",
"- hugo genes averaged and uniqued in TPM space\n",
"- hugo genes summed and uniqued in TPM space\n",
"- log2(n+1) normalization applied\n",
" - File written as rsem.genes.tpm.hugo.log2plus1.dedupe.tab\n"
]
Expand Down Expand Up @@ -140,7 +140,7 @@
"# Takes : dataframe of TPM columns\n",
"# returns : dataframe. \n",
" # finds all row labels that are duplicate\n",
" # averages their values together to create an unique row label\n",
" # sum their values together to create an unique row label\n",
"def uniquify_genes(exp):\n",
" return exp.groupby(exp.index).sum()"
]
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