User: Linda Chaba

gravatar for Linda Chaba
Linda Chaba10
Reputation:
10
Status:
New User
Location:
Kenya
Last seen:
4 months, 1 week ago
Joined:
3 years, 9 months ago
Email:
l*********@gmail.com

Posts by Linda Chaba

<prev • 8 results • page 1 of 1 • next >
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Mathematics behind LIMMA when we have quantitative outcome
... Could someone suggest for me a text explaining in details the mathematics behind LIMMA when we have a quantitative outcome. Most of the available literature I have come across explain LIMMA mathematically when  we have two- sample groups. For example, instead of using D=mean(x)-mean(y), do we use re ...
limma written 2.9 years ago by Linda Chaba10 • updated 2.9 years ago by James W. MacDonald51k
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Comment: C: SAM r for finding up and down regulated genes
... Thank you Valerie for pointing that out.   ...
written 3.7 years ago by Linda Chaba10
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SAM r for finding up and down regulated genes
... I'm using the below code for samr to find down and up regulated genes source("http://bioconductor.org/biocLite.R") biocLite(samr) data=celline.data #expression data imported from excel file whose columns are samples and rows are genes. First row has quantitative outcome. x=data[-1,] #expression ...
samr written 3.7 years ago by Linda Chaba10 • updated 3.7 years ago by Valerie Obenchain6.7k
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Comment: C: Design matrix for continuous independent variable in limma
... Okay. Thanks ...
written 3.8 years ago by Linda Chaba10
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Comment: C: Design matrix for continuous independent variable in limma
... Dear Aaron, One more question. I don't have raw data set.I have  processed (normalized and filtered) data set consisting of log2 rations of 23,360 genes on 35 samples in an excel format. I imported the data the usual way and used it to get a fit object out of lmFit/eBayes. My question is, is it ok ...
written 3.8 years ago by Linda Chaba10
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Comment: C: Design matrix for continuous independent variable in limma
... Thank you Steve.  ...
written 3.8 years ago by Linda Chaba10
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Comment: C: Design matrix for continuous independent variable in limma
... Thank you Aaron for your answer, it was very helpful. However, I'm getting an error (Error: could not find function "topTags") when using "topTags" to get my results. It could be because I'm missing a package. What difference would it have if I use "topTable" to get my results?  I am using limma pac ...
written 3.8 years ago by Linda Chaba10
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Design matrix for continuous independent variable in limma
... I'm using limma for the first time. I have a problem in creating a design matrix. I'm interested in finding genes that are differentially expressed given only one continuous outcome for example age. I have 35 samples. How will my design matrix looks like? Thank you.  ...
microarray limma written 3.8 years ago by Linda Chaba10

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Design matrix for continuous independent variable in limma

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