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INFO:main:Initiating analysis
INFO:main:Loading the read count matrix
INFO:main:Normalizing read counts
INFO:main:Calculating raw fold change for replicate 1
INFO:main:Caculating smoothed Epirical Bayes estimates of stdev for replicate 1
INFO:main:Caculating guide-level Zscores for replicate 1
Traceback (most recent call last):
File "drugz.py", line 478, in
main()
File "drugz.py", line 475, in main
drugZ_analysis(args)
File "drugz.py", line 458, in drugZ_analysis
fold_change =pd.concat(fold_changes, axis=1, sort=False)
TypeError: concat() got an unexpected keyword argument 'sort'

Hi,

I am getting the following error while running drugz. Do you have any idea why it might be happening?

Traceback (most recent call last):
File "/Users/bibaswan/Documents/programs/drugz/drugz.py", line 242, in
main()
File "/Users/bibaswan/Documents/programs/drugz/drugz.py", line 238, in main
args.fc_outfile, remove_genes, args.pseudocount, args.minObs, args.half_window_size, args.index_column, not args.quiet)
File "/Users/bibaswan/Documents/programs/drugz/drugz.py", line 113, in drugz
if (ebstd >= fc[eb_std_samplid][i-1]):
File "/Users/bibaswan/anaconda/lib/python3.5/site-packages/pandas/core/series.py", line 623, in getitem
result = self.index.get_value(self, key)
File "/Users/bibaswan/anaconda/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 2560, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 83, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 91, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 139, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 811, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 817, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 499

Thanks,

Bibaswan

Hi Medina,
When I was running drugZ_w_modules.py, I got the error information:

File "drugZ_w_modules.py", line 347, in drugZ_analysis
fold_change =pd.concat(fold_changes, axis=1, sort=False)
TypeError: concat() got an unexpected keyword argument 'sort'

It is OK when I was using DrugZ.py

Best,
Wenjun

Greetings,

I am trying to run Drugz by using the example provided here (I have copied and pasted the example into a tab-delimited txt file); however, I am getting an error:

python drugz.py -i drugz_trial_unix.txt -o drugz-output.txt -c T15_A_control,T15_B_control -x T15_A_olaparib,T15_B_olaparib

INFO:main:Initiating analysis
INFO:main:Loading the read count matrix
INFO:main:Normalizing read counts
INFO:main:Calculating raw fold change for replicate 1
Traceback (most recent call last):
File "drugz.py", line 478, in
main()
File "drugz.py", line 475, in main
drugZ_analysis(args)
File "drugz.py", line 450, in drugZ_analysis
fc_zscore_id='zscore_fc_{replicate}'.format(replicate=i))
File "drugz.py", line 187, in empirical_bayes
results = fold_change.iloc[no_of_guides - (half_window_size + 1)][empirical_bayes_id]
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 879, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1496, in _getitem_axis
self._validate_integer(key, axis)
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1437, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

I am attaching the input file I tried to use. I have tried both Unix(LF) and Windows(CR LF) formatting, but both led to the same errors.

I will greatly appreciate any help or advice.

Thank you very much.

Regards,
Anna
drugz_trial_unix.txt

Hi,

I'm a bioinformatician developer working at Horizon Discovery and I was recently asked by one of the scientists to explain why FDRs they'd calculated using your software were > 1.

After a bit of digging into the method you were using and the drugz code, I discovered that you're missing the part of the equation that corrects when p * (n/r) is > the the previous p value (in rank order).

I'm more than happy to provide you with some code to pull request which fixes this, it's a little bit more involved, but not overly so, if that's helpful to you.

Regardless, I thought you'd probably want to know.

I've verified my new values using other in-built FDR calculations e.g. R's and they're correct. I can provide the unit tests as well, if they're helpful.

Anyway, just wanted to let you know. Thanks for your time and for contributing so strong to the open source community!

Dr John McGonigle

Hi,

I run the drugz soft on readcount files downloaded from a published study. The soft runs fine with no error and drugz report is complete. However, foldchange file does not output any line.

File IR.drugz-output.tsv contains 17943 lines. Here are the head output of file:

head IR.drugz-output.tsv
GENE sumZ numObs normZ pval_synth rank_synth fdr_synth pval_supp rank_supp fdr_supp
LIG4 -26.06 8 -8.96 1.6e-19 1 2.88e-15 1 17942 1
NHEJ1 -25.13 8 -8.64 2.86e-18 2 2.57e-14 1 17941 1
ATM -19.75 6 -7.83 2.45e-15 3 1.47e-11 1 17940 1
FAM35A -19.65 8 -6.73 8.74e-12 4 3.92e-08 1 17939 1
PNKP -16.08 8 -5.48 2.09e-08 5 7.48e-05 1 17938 1
AMBRA1 -15.48 8 -5.27 6.72e-08 6 0.000201 1 17937 1
C7orf49 -14.39 8 -4.89 4.93e-07 7 0.00126 1 17936 1
C20orf196 -14.25 8 -4.84 6.36e-07 8 0.00131 1 17935 1
RNF168 -14.23 8 -4.84 6.56e-07 9 0.00131 1 17934 1

Files IR.drugz-foldchange.tsv contains 0 lines

I called drugz the following way:
python /ip29/marechal_group/programs/drugz/drugz.py -i Dataset_S1_readcounts.txt -o IR.drugz-output.tsv -f IR.drugz-foldchange.tsv -c S08_NT_T18_A,S08_NT_T18_B -x S08_IR_T18_A,S08_IR_T18_B

Thanks alot for your help,
JF

Hi there,
Thanks for releasing drugz, greatly appreciated.

I have some instances where e.g. one of the treatments or controls is missing. In the paper you stated the paired-sample approach does not appear to offer significant benefits over an unpaired approach: when taking the mean fold change across experimental samples and comparing it to the mean fold change across control samples (Additional file 1: Figure S4A), the results are nearly identical to analysis of three paired samples

I was wondering if there was a way to enable drugz-mean when the number of controls doesn't equal the number of treated samples, to keep my pipeline tidier (i.e. not having to resort to other algorithms)?

Best regards,
Miika