User: Ilario De Toma

Reputation:
10
Status:
New User
Location:
Italy
Last seen:
2 years, 4 months ago
Joined:
6 years, 3 months ago
Email:
i************@gmail.com

Posts by Ilario De Toma

<prev • 7 results • page 1 of 1 • next >
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Problem with link generated with R using the string_db$get_link
... I have always been using those commands in R for getting my protein network to be visualized in the string-db site. However now only the first protein of the list get visualized. > head(list_wttg) list_wttg logFC 1 A2A5R2 2 2 A2AJA9 2 3 O88703 2 4 O88737 2 5 P0 ...
stringdb written 2.4 years ago by Ilario De Toma10
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Comment: C: limma's mroast and romer
... You are right! I forgot the argument contrasts that I used for calling limma's fit. What a stupid mistake! > contrasts Contrasts Levels anti210.healthy - scr.healthy anti210.healthy 1 scr.healthy -1 Now ...
written 4.0 years ago by Ilario De Toma10
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Comment: C: limma's mroast and romer
... As regards the value for PropUp, if i have well understood stands for "proportion up", so simply by looking at the topTable of those genes I know that are 11 out of 14 for the M1 gene set and 14 our of 24 for M2. Here is my design matrix, which is the same between the mroast and romer calls. > ...
written 4.0 years ago by Ilario De Toma10
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Comment: C: limma's mroast and romer
... Since my genes for the example are distributing on the top of the ranked list I woukd expect anyway romer "up p value" to be lower than the "down p value" but I am seeing exactly the opposite! ...
written 4.0 years ago by Ilario De Toma10
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limma's mroast and romer
... Hi, I am puzzled by the apparently opposite results in mroast and romer functions from limma. If I well understood the difference is that romer is optimized for a gsea analysis on dataset of gene sets and use sample label rotations, while mroast use rotations of genes and is suitable to test one or ...
limma mroast romer written 4.0 years ago by Ilario De Toma10 • updated 4.0 years ago by Gordon Smyth38k
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Problem in updating AnnotationDbi
... Hi, I cannot update the annotationDbi package to its 1.30.1, when I try to donwload it from biocLite it retrieve the 1.28.2 version. I do not understand why since my R version is > 2.7.0. That's the code I used: R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundati ...
annotationdbi written 4.2 years ago by Ilario De Toma10 • updated 4.2 years ago by James W. MacDonald51k
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2x3 factorial experiment
... I have performed a microarray experiment comparing primary monocyte from mouse fetal livers. I have three KO samples vs. three WT samples (biological replicates). Each sample have been splitted into three plates: - 1/3 (P) have been collected while proliferating (bacteria plate with GM-CSF) -1/3 (U ...
microarray written 6.3 years ago by Ilario De Toma10 • updated 6.3 years ago by James W. MacDonald51k

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For limma's mroast and romer

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