User: Lisa Cohen

gravatar for Lisa Cohen
Lisa Cohen50
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50
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Location:
United States
Last seen:
2 years, 2 months ago
Joined:
4 years, 1 month ago
Email:
l*****************@gmail.com

Posts by Lisa Cohen

<prev • 6 results • page 1 of 1 • next >
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limma::plotMA displays one sample vs. others
... Hello! What is the true definition of MA plot? The limma::plotMA displays Expression log-ratio of one sample vs. others even with NGS platform data. My understanding is this package was developed for microarrays with two-color data and MA plots then were useful to see one sample/array vs. others. I ...
limma plotma written 2.2 years ago by Lisa Cohen50 • updated 2.2 years ago by Gordon Smyth32k
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RNA-Seq fold change compared to control, without replicates
... I am analyzing a set of RNA-Seq data without replicates, possibly using edgeR. (We understand limitations and are only interested in descriptive analyses.) There are three different treatments (OC, OD, UD) and one control (UC). For each treatment, I want to find transcripts with highest and lowest ...
edger written 3.9 years ago by Lisa Cohen50 • updated 3.9 years ago by Dario Strbenac1.4k
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help with limma design, contrast matrices
... I have a set of microarray data (one-channel custom Agilent) that I'm trying to analyze for gene expression differences following an experiment: Sponges were acutely exposed to combinations of oil and dispersant treatments. There were 4 treatment groups: OD, OC, UD, UC, 6 sponge colonies each fragm ...
microarray limma written 4.1 years ago by Lisa Cohen50 • updated 4.1 years ago by Ryan C. Thompson6.1k
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Comment: C: Cannot upgrade bioconductor from 2.12 to 2.13
... Thank you Levi and Julie, I had the same problem last week also but it did not seem to get in the way of my work. Per your suggestion, I tried biocLite("BiocUpgrade") and it worked fine just now on Linux Ubuntu 13.04. The upgrade, however, removed the arrayQualityMetrics package I have been working ...
written 4.1 years ago by Lisa Cohen50
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arrayQualityMetrics - undefined columns selected
... Hi, I'm trying to find the best way to do a quality assessment of a microarray data set. I made the ExpressionSet from scratch (output below), since data were collected with a custom Agilent microarray. Using the most updated version of the arrayQualityMetrics package (downloaded yesterday, 16 Octo ...
microarray arrayqualitymetrics written 4.1 years ago by Lisa Cohen50 • updated 4.1 years ago by Wolfgang Huber13k
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Biobase - Error: ExpressionSet
... I'm using the Biobase package to build an ExpressionSet from scratch using data from a custom 8x15k Agilent microarray. I'm getting this error and can't quite figure it out. Does anyone know how *phenoData* can extend the * annotation*? I would like to connect *phenoData* to *exprs* with the Chip an ...
microarray annotation go experimentdata biobase written 4.1 years ago by Lisa Cohen50 • updated 4.1 years ago by Laurent Gatto840

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