Comments (5)
Akanksha2511
commented on July 17, 2024
Hi,
You can ignore the runtime warning. It occurs when division by zero is encountered.
NA means that HOME did not find any significant DMR for that sample comparison. Will update that on the documentation. Also, if you are getting too many NAs it might be worth trying running HOME pairwise for multiple samples. So, if you run the same sample file path used for timeseries in normal HOME pairwise mode you will get DMRs for each comparison and then you can merge them to get the final DMRs for all sample comparison. Please let me know if you have any other issues/doubts.
Thanks,
Akanksha
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bhofmei
commented on July 17, 2024
Thank you for the explanation. I was guessing that NA meant it wasn’t signficant but then I didn’t understand why the DMR would be included in the output when it was NA at all comparisons.
I had tried the pairwise technique before but was struggling to elegantly merge the DMRs afterwards and comparisons afterwards. It appears that bedtools merge would work to find a master list of DMRs and maybe say what comparison it came from, but it’s still not elegant since the new DMR boundaries, and potentially multiple testing correction, could change the statistical significance. My data is definitely time series, so if I were to use this technique, would you suggest merging from all comparisons or only the timeseries-relevant ones?
… On Oct 11, 2018, at 7:19 PM, Akanksha2511 ***@***.***> wrote:
Hi,
You can ignore the runtime warning. It occurs when division by zero is encountered.
NA means that HOME did not find any significant DMR for that sample comparison. Will update that on the documentation. Also, if you are getting too many NAs it might be worth trying running HOME pairwise for multiple samples. So, if you run the same sample file path used for timeseries in normal HOME pairwise mode you will get DMRs for each comparison and then you can merge them to get the final DMRs for all sample comparison. Please let me know if you have any other issues/doubts.
Thanks,
Akanksha
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Akanksha2511
commented on July 17, 2024
Hard to say, without looking into the data. I would suggest merging for all comparisons, otherwise, how would you find the time series-relevant ones?.
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bhofmei
commented on July 17, 2024
Okay thank you! I'll try that. FWIW, it would be awesome if you added some sort of try-catch or error check for the the divisible by zero error. Otherwise it's difficult to tell if the program actually finished and finished correctly.
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Akanksha2511
commented on July 17, 2024
yes sure. Thanks
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Related Issues (20)
- training data CG and non-CG for arabidopsis HOT 1
- HOME-timeseries error HOT 2
- sample path HOT 1
- cannot open file './scripts/HOME_R.R': No such file or directory HOT 1
- HOME-pairwise script is missing HOT 1
- HOME run does not end HOT 6
- Error when finding DMR's with scaffolded genome HOT 4
- multiprocessing range parameter HOT 3
- Issue 20# Home run doesn’t end HOT 6
- HOME-pairwise for different numbers of replicate HOT 4
- HOME ubale to open X server HOT 1
- HOME_DMR error HOT 1
- All Comb1-n "NA" for most DMRs in CHH HOT 8
- Push more
- Nanopore data? HOT 2
- NameError: name 'status' is not defined HOT 2
- HOME-timeseries Exception HOT 4
- Exception: reduce() of empty sequence with no initial value
- Installation Error
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