User: António Miguel de Jesus Domingues
- Reputation:
- 470
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- Location:
- Germany
- Website:
- http://adomingues.gith...
- Last seen:
- 1 day, 23 hours ago
- Joined:
- 7 years, 7 months ago
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Posts by António Miguel de Jesus Domingues
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... Got it! For future reference, and in case someone else stumbles upon this, this is the final version of the commands I used:
```R
fullCov <- fullCoverage(
files = files,
chrs = chrom,
L = read_length,
verbose = TRUE,
totalMapped = total_mapped,
targetSize = targetSize,
filte ...
written 28 days ago by
António Miguel de Jesus Domingues • 470
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... > It seems that you are normalizing your data twice, no?
That seems to have been the major issue. Once I remove filterring from the `fullCoverage` it all started to make sense.
> The code you provided, is that the correct version? You should be getting an error when you run regionMatrix(fil ...
written 4 weeks ago by
António Miguel de Jesus Domingues • 470
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... I have been trying to leverage `definder`'s ability to detect expression without the need of an annotation to identify broad regions of expressions that we observe in certain conditions:
(not s ...
written 5 weeks ago by
António Miguel de Jesus Domingues • 470
• updated
5 weeks ago by
Leonardo Collado Torres • 690
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... I am starting to use the `DEP` [package][1] for analysis of differentially enriched proteins, and so far I am quite happy with it. The vignette is quite good and all the functions worked without issues.
I am however confused about the meaning of the columns in the output results generated by `get_d ...
written 3 months ago by
António Miguel de Jesus Domingues • 470
• updated
12 weeks ago by
arne.smits • 60
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... I am also having problems replicating it so it is likely that at some I made a mistake. I will add a note at the top of the post. Apologies for the time lost but I was certain that something was going on.
...
written 10 months ago by
António Miguel de Jesus Domingues • 470
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... I actually tried to create a smaller example in the same way, and like you also failed. That is why I mention that this could be a localized issue. That said, I will try to replicate with a small subset of and get back to you.
...
written 10 months ago by
António Miguel de Jesus Domingues • 470
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... See my answer here: https://www.biostars.org/p/351612/#352575
...
written 10 months ago by
António Miguel de Jesus Domingues • 470
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... IGNORE this issue. It is likely that I did something wrong at some point since I am having problems reproducing the problem myself.
tldr: it seems that after `collapseReplicates` the levels of newly created factors are shifted affecting the results. **If** this observation is correct and not a d ...
written 10 months ago by
António Miguel de Jesus Domingues • 470
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... Hi konstatinos,
The majority of reads multimap to different piRNAs, I took the sum of reads assigned to each piRNA (both unmatched/matched reads to the genome).
Maybe I misunderstood, but does this mean that a read is counted more than once? Each read should be counted only once. If you want to u ...
written 10 months ago by
António Miguel de Jesus Domingues • 470
0
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... Sorry for the belated reply, but working on other things got in the way. Thank your for the clarification regarding the separate call for each range - I had no idea it worked that way. For now I am sticking with GenomicAlignments followed by GR. Memory might be an issue down the line, but having re ...
written 11 months ago by
António Miguel de Jesus Domingues • 470
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