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Blaise LI
bioinfo_utils
Commits
88623070
Commit
88623070
authored
Jan 08, 2020
by
Blaise Li
Browse files
Avoid error when not enough data in log10.
parent
7f6056dc
Changes
1
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RNA_Seq_Cecere/RNA-seq.snakefile
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88623070
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@@ -1276,8 +1276,14 @@ rule compare_replicates:
(r_val, p_val) = pearsonr(data[rep_a], data[rep_b])
corr_file.write(f"{rep_a}{warn_a}_vs_{rep_b}{warn_b}\t{r_val} ({p_val})\n")
filtered = log_data[[rep_a, rep_b]].dropna()
(log_r_val, log_p_val) = pearsonr(filtered[rep_a], filtered[rep_b])
corr_file.write(f"log10_{rep_a}{warn_a}_vs_log10_{rep_b}{warn_b}\t{log_r_val} ({log_p_val})\n")
try:
(log_r_val, log_p_val) = pearsonr(filtered[rep_a], filtered[rep_b])
corr_file.write(f"log10_{rep_a}{warn_a}_vs_log10_{rep_b}{warn_b}\t{log_r_val} ({log_p_val})\n")
except ValueError as err:
if str(err) == "x and y must have length at least 2.":
corr_file.write(f"Only {len(filtered)} points in log10 data.\n")
else:
raise
corr_file.write("(*): not normal\n(**): log10 not normal\n")
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