biopyju
commented
1 year ago Hello,
Like claus-h-g, thank you for methylprep! Same question as claus-h-g. I tried to analyse .IDATs from Infinium MethylationEPIC v2.0, provided by a NextSeq 550 with methylprep.run_pipeline(path, export=True, betas=True, m_value=True, poobah=True, export_poobah=True, meta_data_frame=True), but I've an error :
`--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[3], line 1 ----> 1 methylprep.run_pipeline(path, export=True, betas=True, m_value=True, poobah=True, export_poobah=True, meta_data_frame=True)
File c:\Users\cal19499\Documents\A\anaconda3.10\lib\site-packages\methylprep\processing\pipeline.py:321, in run_pipeline(data_dir, array_type, export, manifest_filepath, sample_sheet_filepath, sample_name, betas, m_value, make_sample_sheet, batch_size, save_uncorrected, save_control, meta_data_frame, bit, poobah, export_poobah, poobah_decimals, poobah_sig, low_memory, sesame, quality_mask, pneg_ecdf, file_format, **kwargs) 318 missing_probe_errors = {'noob': [], 'raw':[]} 320 for batch_num, batch in enumerate(batches, 1): --> 321 idat_datasets = parse_sample_sheet_into_idat_datasets(sample_sheet, sample_name=batch, from_s3=None, meta_only=False, bit=bit) # replaces get_raw_datasets 322 # idat_datasets are a list; each item is a dict of {'green_idat': ..., 'red_idat':..., 'array_type', 'sample'} to feed into SigSet 323 #--- pre v1.5 --- raw_datasets = get_raw_datasets(sample_sheet, sample_name=batch) 324 if array_type is None: # use must provide either the array_type or manifest_filepath.
File c:\Users\cal19499\Documents\A\anaconda3.10\lib\site-packages\methylprep\models\sigset.py:106, in parse_sample_sheet_into_idat_datasets(sample_sheet, sample_name, from_s3, meta_only, bit) 104 batch_probe_counts.add(n_snps_read) 105 counts_per_sample[n_snps_read] += 1 --> 106 idat_datasets[idx]['array_type'] = ArrayType.from_probe_count(n_snps_read) 107 if len(batch_probe_counts) != 1: 108 array_types = Counter([dataset['array_type'] for dataset in idat_datasets])
File c:\Users\cal19499\Documents\A\anaconda3.10\lib\site-packages\methylprep\models\arrays.py:46, in ArrayType.from_probe_count(cls, probe_count) 43 LOGGER.warning(f'Probe count ({probe_count}) falls outside of normal range. Setting to newest array type: EPIC') 44 return cls.ILLUMINA_EPIC ---> 46 raise ValueError(f'Unknown array type: ({probe_count} probes detected)')
ValueError: Unknown array type: (1105209 probes detected)`
With GenomeStudio I don't have the same number of probes (937055)...
If someone know how to solve this issue... Thank you!
Leo-GG
parlar
isycara
eliopato
brj0
petermchale
Hello Many thanks for providing methylprep. May I ask if the analysis of files originating form Infinium MethylationEPIC v2.0 chips is already possible?