From ec407abeaed4e0b5a158c92e0270593f9f172955 Mon Sep 17 00:00:00 2001 From: "Daniel J. B. Clarke" Date: Mon, 16 Oct 2023 10:03:44 -0400 Subject: [PATCH] Fixes #892 --- appyters/Bulk_RNA_seq/appyter.json | 2 +- appyters/Bulk_RNA_seq/utils.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/appyters/Bulk_RNA_seq/appyter.json b/appyters/Bulk_RNA_seq/appyter.json index ed3b1eab..dd36cabc 100644 --- a/appyters/Bulk_RNA_seq/appyter.json +++ b/appyters/Bulk_RNA_seq/appyter.json @@ -2,7 +2,7 @@ "$schema": "https://raw.githubusercontent.com/MaayanLab/appyter-catalog/main/schema/appyter-validator.json", "name": "Bulk_RNA_seq", "title": "Bulk RNA-seq analysis pipeline", - "version": "0.1.7", + "version": "0.1.8", "description": "Bulk RNA-seq analysis pipeline enables you to analyze and visualize datasets with state-of-the-art algorithms and visualization methods.", "image": "screenshot.png", "authors": [ diff --git a/appyters/Bulk_RNA_seq/utils.py b/appyters/Bulk_RNA_seq/utils.py index 15604320..fdc40d8e 100644 --- a/appyters/Bulk_RNA_seq/utils.py +++ b/appyters/Bulk_RNA_seq/utils.py @@ -424,7 +424,7 @@ def get_signatures(classes, dataset, normalization, method, meta_class_column_na elif method == "edgeR": edgeR = robjects.r['edgeR'] - edgeR_results = pandas2ri.conversion.rpy2py(edgeR(pandas2ri.conversion.py2rpy(expr_df), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids))) + edgeR_results = pandas2ri.conversion.rpy2py(edgeR(pandas2ri.conversion.py2rpy(expr_df.loc[:, cls1_sample_ids+cls2_sample_ids]), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids))) signature = pd.DataFrame(edgeR_results[0]) signature.index = edgeR_results[1] @@ -432,7 +432,7 @@ def get_signatures(classes, dataset, normalization, method, meta_class_column_na elif method == "DESeq2": # deseq2 receives raw counts DESeq2 = robjects.r['deseq2'] - DESeq2_results = pandas2ri.conversion.rpy2py(DESeq2(pandas2ri.conversion.py2rpy(expr_df), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids))) + DESeq2_results = pandas2ri.conversion.rpy2py(DESeq2(pandas2ri.conversion.py2rpy(expr_df.loc[:, cls1_sample_ids+cls2_sample_ids]), pandas2ri.conversion.py2rpy(cls1_sample_ids), pandas2ri.conversion.py2rpy(cls2_sample_ids))) signature = pd.DataFrame(DESeq2_results[0]) signature.index = DESeq2_results[1]