User: José Luis Lavín
José Luis Lavín • 10
- Reputation:
- 10
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- Location:
- Spain
- Last seen:
- 1 year, 9 months ago
- Joined:
- 7 years, 2 months ago
- Email:
- j******@cicbiogune.es
Posts by José Luis Lavín
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Comment:
C: ATACseqQC memory overflow issue
... Dear Jianhong,
I have tried the following script (the bamQC command actually worked). I tried your suggestion using only a couple of chromosomes (e.g. 1 and 2) and it crashes at the a point a little bit further...
library(ATACseqQC)
library(ChIPpeakAnno)
library(BSgenome.Hsapiens.UCSC.hg19)
libra ...
written 21 months ago by
José Luis Lavín • 10
0
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2
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... Dear All,
I'm trying to analizesome ATAC-seq samples using the ATACseqQC package and I am unable to make it work correctly.
The proccess always crashes when I reach the same part of the workflow shown in the vignette this function
fragSize <- fragSizeDist(bamfile, bamfile.labels)
After a whi ...
written 22 months ago by
José Luis Lavín • 10
• updated
21 months ago by
Haibo.Liu • 0
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... Dear Gordon,
I totally agree with you.
This time, I asked in this list because I needed a clear explanation and a solution for the nth issue with this code...Since I do not have to use it frequently, I never seem to find the time to invest into reprograming this pipeline.
Please accept my apologi ...
written 3.5 years ago by
José Luis Lavín • 10
0
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1
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1
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... Dear Gordon,
Thank you for your swift answer.
I recreated the object and got the following fit:
> show(fit)
[[1]]
An object of class "MArrayLM"
$coefficients
g1 g2
ILMN_2417611 7.933408 7.760932
ILMN_2896528 9.382122 9.390301
ILMN_2721178 7.462175 7.456717
ILM ...
written 3.5 years ago by
José Luis Lavín • 10
0
votes
1
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805
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... Here is my session info (I couldn't include it in the previous post...
And here is my session info:
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252
[4] LC_NUMERIC=C ...
written 3.5 years ago by
José Luis Lavín • 10
2
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1
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805
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1
answer
... *Question posted as new question thread as requested by Aaron Lun*
Dear limma team,
First of all, I want to thank you for this wonderful package. This said, I need to ask you a question on the subject mentioned in this post, Standard error calculation from my fit object using the command in the po ...
written 3.5 years ago by
José Luis Lavín • 10
0
votes
3
answers
765
views
3
answers
... Here is my session info (I couldn't include it in the previous post...
And here is my session info:
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252
[4] LC_NUMERIC=C ...
written 3.5 years ago by
José Luis Lavín • 10
0
votes
3
answers
765
views
3
answers
... Dear limma team,
First of all, I want to thank you for this wonderful package. This said, I need to ask you a question on the subject mentioned in this post, Standard error calculation from my fit object using the command in the post:
>std.error = fit$stdev.unscaled * fit$sigma
> std.error ...
written 3.5 years ago by
José Luis Lavín • 10
0
votes
3
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1.3k
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3
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... Thank you Guangchuang Yu!
Explicitly calling print(dotplot()) and print(barplot()), did the trick and allowed me to obtain the graphics inside the FOR loop.
Thank you also for this remarkable package
Best wishes
JL
...
written 3.6 years ago by
José Luis Lavín • 10
0
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3
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1.3k
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3
answers
...
Dear Guangchuang Yu,
I did that in a previous version of the code, and I did confirm my lists entered the loop (In fact, as I said before, lists are processed and the different csv tables are retrieved. The problem comes when the plotting functions try to find the objects such as "egoBP".
Is at t ...
written 3.6 years ago by
José Luis Lavín • 10
Latest awards to José Luis Lavín
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created a question with more than 1,000 views.
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