User: Mark Reimers

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Mark Reimers70
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Posts by Mark Reimers

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High-Throughput Data Analysis Course Announcement: Cold Spring Harbor Labs - June 14-27
... This course will assist people just getting started in Bioconductor. It is designed for people who have some statistical or computational background, but are not experienced bioconductor users. See http://meetings.cshl.edu/courses/c-data06.shtml. INTEGRATED DATA ANALYSIS FOR HIGH THROUGHPUT BIOLOGY ...
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RE: correcting for 3' bias in highly amplified RNA samples
... Hello Ben, Our collaborators have been taking microdissected samples and amplifying them. We find that the distribution of probe intensities in a probe set is greatly affected; the signal from 5' probes is much decreased. However if the amplifications are done carefully, the amplified samples can be ...
probe affy written 14.9 years ago by Mark Reimers70 • updated 14.9 years ago by Wittner, Ben290
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RE: Advice on print-tip normalization
... Hello Gene, I don't have any advice but some related observations based on looking at regional biases on spotted microarrays. In the slide data that have come in, there seems often to be a bias toward red on the top and bottom edges of the print-tip groups, and a bias toward green in the middle of t ...
cancer probe marray oligo written 15.1 years ago by Mark Reimers70 • updated 15.1 years ago by Gene Cutler50
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RE: RMA normalization
... Hello Hairong, Adai, That suggestion was mine a few weeks ago. My thinking currently is that we may reasonably expect different cell types to have different distributions of RNA abundances; as an extreme example, some cells specialize in making one protein for export. Then it seems to me our best sh ...
normalization cancer written 15.1 years ago by Mark Reimers70 • updated 15.1 years ago by Wolfgang Huber13k
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RE: quantile normalization
... How different are your 'biologically different' samples? In our experience quantile-normalizing across very different samples makes a noticeable difference in relative expression within fairly similar samples. Our main data is cancer cell lines from 9 different tissues, and we find considerable dif ...
normalization cancer process written 15.1 years ago by Mark Reimers70 • updated 15.1 years ago by H. Han30
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RMA and quantile normalisation
... Hello Arne, Several publications recently have shown that the distribution of gene abundances seems to follow a power law (one such is referenced at www.the-scientist.com. This should turn into an exponential density on the log scale we often use. The 'hump' we see in signal intensities from microar ...
probe written 15.6 years ago by Mark Reimers70
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RE: AffyPLM
... > -----Original Message----------- Message: 1 Date: Mon, 1 Mar 2004 16:08:45 +0100 From: Subject: RE: [BioC] AffyPLM To: , , , Message-ID: Content-Type: text/plain; charset="iso-8859-1" If the horizontal striping (due to the scanner) is a systematic error, then one do ...
cancer written 15.6 years ago by Mark Reimers70

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