User: Mattia

gravatar for Mattia
Mattia10
Reputation:
10
Status:
New User
Location:
Milano
Last seen:
4 days, 12 hours ago
Joined:
3 years, 6 months ago
Email:
m************@hotmail.it

Posts by Mattia

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Analyzing (HiSeq) PANCAN data set RNA-seq data using DaMiRseq
... Dear Daedalus, sorry for the delay. Probably, the notification of your post ended up in my SPAM. Regarding your problem, I think that your countdata file is not well formatted. I guess because of one of these two reasons: 1) some elements of the count matrix are not integer; 2) countdata has some n ...
written 6 weeks ago by Mattia10
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... I installed this version and it works perfectly!. Thanks again Andrzej! Mattia. ...
written 2.7 years ago by Mattia10
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Answer: A: Error occurred, creating Vignette in LateX style 2.0
... Following David Carlisle suggestion, in TeX - LaTeX Stack Exchange Furum, now the problem seems to be solved;  I set a new Path in "Root" panel of Miktek Settings: C:\Program Files\R\R-3.3.2\library\BiocStyle\resources Then, I modified two lines in 'myPackage.Rnw' : \RequirePackage[]{Bioc ...
written 2.7 years ago by Mattia10
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... No Andrzej, nothing changes. But I tried to comment in .tex file: %\RequirePackage[]{C:/Program Files/R/R-3.3.2/library/BiocStyle/resources/tex/Bioconductor2} %\AtBeginDocument{\bibliographystyle{C:/Program Files/R/R-3.3.2/library/BiocStyle/resources/tex/unsrturl}} and  %\author{first auth} % ...
written 2.7 years ago by Mattia10
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... You are right Martin: it's strange. I'm going to check LateX options. Anyway: here my .tex file: %\VignetteIndexEntry{Vignette of "myPackage" package} %\VignettePackage{myPackage} %\VignetteEngine{knitr::knitr} % To compile this document % library('knitr'); rm(list=ls()); knit('myPackage.Rnw') \ ...
written 2.7 years ago by Mattia10
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Comment: C: Error occurred, creating Vignette in LateX style 2.0
... Andrzej it's exactly the same: ! LaTeX Error: File `C:/ProgramFiles/R/R-3.3.2/library/BiocStyle/resources/tex/Bioconductor.sty' not found.   ...
written 2.7 years ago by Mattia10
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Error occurred, creating Vignette in LateX style 2.0
... Hi, I created a package which I would submit in Bioconductor. I followed guidelines: regarding "code" I haven't got any errors or "warning" and each function seems to work perfectly. Then for each function, I created .Rd files, using Roxygen2. Again, no errors and no warning, when I "Build" and whe ...
biocstyle build/check error vignettes latex written 2.7 years ago by Mattia10 • updated 2.7 years ago by Andrzej Oleś720
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Comment: C: SVA and proportion of variance explained
... Jeff, I followed your suggestion. I created a simulated RNA-Seq dataset (15000 genes and 30 samples for each of the 2 conditions) with 3 batch effects (strong, medium and weak effects). Then, after VST normalization, I calculated: uu_val, as discussed above; uu_val2 <-uu$values^2 / sum(uu$va ...
written 2.8 years ago by Mattia10
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Comment: C: SVA and proportion of variance explained
... Thanks Jeff for your precious suggestion. Actually, I tried to do something similar to PCA, using a part of your "sva code": dat <- data_normalized pprob <- svaobj$pprob.gam*(1-svaobj$pprob.b) dats <- dat*pprob dats <- dats - rowMeans(dats) uu <- eigen(t(dats)%*%dats) I added this l ...
written 2.8 years ago by Mattia10
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SVA and proportion of variance explained
... Hi guys, I'm using SVA package for identifying unwanted variation and then removing batch effects from my RNA-Seq data. Let's say I found my ten SV with sva function; my question is: how can I calculate the  proportion of variance explained for each SV, as for PCs in PCA? Thanks a lot, Mattia ...
sva pca svd explained variance written 2.8 years ago by Mattia10 • updated 2.8 years ago by Jeff Leek560

Latest awards to Mattia

Popular Question 20 months ago, created a question with more than 1,000 views. For edgeR GLM fitted values
Popular Question 20 months ago, created a question with more than 1,000 views. For SVA and proportion of variance explained

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