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jerry ☆ Russia, 2015-07-10 17:23 (3577 d 11:30 ago) Posting: # 15065 Views: 7,003 |
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What about my problem with 2x2x4 design , i decided it, it was simple problem. But now, when i get all data, i try process it, but after i choose my csv file, R crash with this error Error in LL[, 2] : subscript out of bounds Please help. thats my scan of setting ![[image]](img/uploaded/image117.jpg) and my dataset https://www.sendspace.com/file/nwuk5r also i can give and that error Error in SeqLeg[[2]] : subscript out of bounds Edit: category changed [Ohlbe] |
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mittyri ★★ Russia, 2015-07-11 00:51 (3577 d 04:02 ago) @ jerry Posting: # 15066 Views: 5,768 |
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Hi Jerry! I didn't have sufficient time to answer to your previous post. It's solved by yourself and it's very good  About your current problem: On this forum you can find some discussions about Bear's features. At this moment I wouldn't recommend you to use Bear for replicate studies with incomplete data (there are some skipped periods in your data - see subjs #18 & 19) The Bear is a very good package, BTW it is not validated by now and has some known bugs and restrictions (so pity...) — Kind regards, Mittyri |
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jerry ☆ Russia, 2015-07-11 10:35 (3576 d 18:18 ago) @ mittyri Posting: # 15067 Views: 5,848 |
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Dear, mittyri. Thank you. You right, because for subjects 18 and 19 there is no data for Cmax. For example in one period Cmax=0, so we have 20 parts time from 0 to 12 (0,0.25.....12) and Cmax=0. I read hear http://pkpd.kmu.edu.tw/bear/ When a drug plasma/serum/blood concentration is near the end of sampling time and is below LLOQ, this value (entire row) can be deleted if the IndivDP_output function will not be used; The recommended way is to input these data values as 'NA' since bear will handle it properly. However, the first data point at (time = 0, Cp = 0) must be included; So that why i deleted this rows and noted as NA What do you recommend me? Indeed these results were processed by another man, i just try repeat his result, but, let's initially view just only one subject, lets' #2 and try process it, after we can see these parameters ![[image]](img/uploaded/image118.jpg) In report, for 2 subject another results 1 1 1 Auc0T=7347 1 sequence 1 period and reference drug. After my analysis 1 sequence 1 period and reference drug AucoT=7244 for another periods the results from that man and my are different too here the data http://rghost.ru/6jxsT9y7c what about 18 and 19, as i right understood these data were excluded from analysis. So i have design 2x2x4! But how correct process it. For 2 subject after process, R writes --------------------------------------------------------------------------- 1. xxx_nca_pk.txt: --> Cmax, Tmax, AUC0t, AUC0inf, AUC0t/AUC0inf, ln(Cmax), ln(AUC0t), ln(AUC0inf), MRT0inf, T1/2(z), Vd/F, lambda_z, and Cl/F --> PK parameter summary (NCA outputs) 2. xxx_conc_time_plots.pdf: individual linear and semilog plots, spaghetti plots, and mean conc. plots. 3. xxx_stat_sum.txt **************************************************************************** Error in SeqLeg[[2]] : subscript out of bounds did i correct change 0 for Cmax on NA? |
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mittyri ★★ Russia, 2015-07-11 17:05 (3576 d 11:47 ago) @ jerry Posting: # 15068 Views: 5,747 |
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Hi Jerry! I didn't catch all your suggestions despite my efforts, sorry...  When I mentioned the incomplete data, I had in mind the quantity of periods. Let's look at your data one more time: there is no data for period 2 by subject #18 and no data for period 3 by subject #19 I see the only one way in Bear to solve this: to remove all data of subjects #18&19 from analysis. BTW if you need NCA data only, you can input some "artificial" data for missing periods. Then you can get NCA data and remove the results for "artificial" periods. Of course the statistical analysis won't be performed in this way. That's why I recommended not to use current Bear for this dataset (and all data sets with incomplete replicate data). You can use another software (only payware, yes  ) ❝ In report, for 2 subject another results ❝ 1 1 1 Auc0T=7347  ❝ For 2 subject after process, R writes ❝ Error in SeqLeg[[2]] : subscript out of bounds Did you try to perform NCA analysis in Bear for 1 subject? I think Bear was a little bit confused with sequence. ❝ did i correct change 0 for Cmax on NA? — Kind regards, Mittyri |
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jerry ☆ Russia, 2015-07-11 18:02 (3576 d 10:51 ago) @ mittyri Posting: # 15069 Views: 5,769 |
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❝ Did you try to perform NCA analysis in Bear for 1 subject? I think Bear was a little bit confused with sequence. Yes, mittyri. i performed analysis only for 1 subject(#2) and i think that man did so. Maybe he did analysis for all 24 subjects separately. Do you consider that error concerned with it? I should use not only one subject? ❝ ❝ did i correct change 0 for Cmax on NA? ❝ I didn't understand where and what did you change. As you cited Bear manual "near the end of sampling time and is below LLOQ... input these data values as 'NA'..." Cmax cannot be changed to NA, isn't it? If I understood correctly, if Cmax=0 and Cmax < LLOQ i can delete entire row. the row consist of 6 digits (subject,seq,prd,tmt, t,conc |
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yjlee168 ★★★   Kaohsiung, Taiwan, 2015-07-14 11:22 (3573 d 17:30 ago) @ jerry Posting: # 15081 Views: 5,571 |
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Dear jerry, ❝ If I understood correctly, if Cmax=0 and Cmax < LLOQ i can delete entire row. ❝ ... Not just to delete the entire row, but all period data of that subject. Cmax can not be zero or 'NA' in dataset; otherwise, it will crash when taking logarithm of Cmax. — All the best, -- Yung-jin Lee bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan https://www.pkpd168.com/bear Download link (updated) -> here |
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