User: José Luis Lavín

gravatar for José Luis Lavín
Reputation:
10
Status:
New User
Location:
Spain
Last seen:
8 months, 3 weeks ago
Joined:
6 years, 1 month ago
Email:
j******@cicbiogune.es

Posts by José Luis Lavín

<prev • 21 results • page 1 of 3 • next >
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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 9 months ago by José Luis Lavín • 10
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ATACseqQC memory overflow issue
... 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 ...
software error atac-seq atacseqqc written 9 months ago by José Luis Lavín • 10 • updated 9 months ago by Haibo.Liu • 0
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Comment: C: Problem obtaining standard error from limma
... 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 2.4 years ago by José Luis Lavín • 10
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Comment: A: Problem obtaining standard error from limma
... 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" $coefficients g1 g2 ILMN_2417611 7.933408 7.760932 ILMN_2896528 9.382122 9.390301 ILMN_2721178 7.462175 7.456717 ILM ...
written 2.4 years ago by José Luis Lavín • 10
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Comment: C: Problem obtaining standard error from limma
... Here is my session info (I couldn't include it in the previous post... And here is my session info: Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 [4] LC_NUMERIC=C                   ...
written 2.4 years ago by José Luis Lavín • 10
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Problem obtaining standard error from limma
... *Question posted as new question thread as requested by Aaron Lun* Dear limma team, First of all, I want to thank you for this wonderful package. This said, I need to ask you a question on the subject mentioned in this post, Standard error calculation from my fit object using the command in the po ...
limma standard error written 2.4 years ago by José Luis Lavín • 10
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Comment: C: extracting cpm expression from limma fit
... Here is my session info (I couldn't include it in the previous post... And here is my session info: Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 [4] LC_NUMERIC=C                   ...
written 2.4 years ago by José Luis Lavín • 10
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Answer: A: extracting cpm expression from limma fit
... Dear limma team, First of all, I want to thank you for this wonderful package. This said, I need to ask you a question on the subject mentioned in this post, Standard error calculation from my fit object using the command in the post: >std.error = fit$stdev.unscaled * fit$sigma > std.error ...
written 2.4 years ago by José Luis Lavín • 10
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Answer: A: Problem retrieving graphics in clusterprofiler
... 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 2.5 years ago by José Luis Lavín • 10
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Comment: C: Problem retrieving graphics in clusterprofiler
... 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 2.6 years ago by José Luis Lavín • 10

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Assign genes to CpG islands
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