User: Mark Baumeister

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Posts by Mark Baumeister

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converting intensity values to log ratios?
... Hi all, I am trying to convert RMA normalized intensity values in my matrix (generated from Affymetirx raw .CEL data composed of ~30 tumor samples and 7 normal samples) to log ratios in which the intensity values from each tumor sample are compared with a reference sample (in this case I chose one ...
convert written 7.9 years ago by Mark Baumeister40
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displaying clustering results in TreeView or MapleTree
... Hi all, I am having trouble viewing the full color spectrum (I only see "red") for data that I have clustered using the hopach method and displaying in either MapleTree or TreeView. When I use the golub or kidney data sets ("Bioconductor" examples) I have no problem seeing the different colors (gre ...
microarray clustering kidney ovarian probe hopach written 7.9 years ago by Mark Baumeister40
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Comment: C: selecting/filtering probesets from exprSet object prior to diff. exp. anal.
... Thanks a lot, James for your help. That seems pretty straightforward. That said, both ExpressionSets and MArrayLM objects (the output from eBayes()) can be subset using the conventional square-bracket functions in R. So for example, you could remove the first ten probesets from your fit2 object thu ...
written 8.0 years ago by Mark Baumeister40
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selecting/filtering probesets from exprSet object prior to diff. exp. anal.
... Hi all, I am new to this list and have a question (below) related to - selecting/filtering probesets from exprSet object prior to diff. exp. anal. I'm also new to Bioconductor and am currently learning preprocessing of microarray data (i.e. raw CEL files from the Affymetrix UG-133A array) and then ...
preprocessing genefilter limma written 8.0 years ago by Mark Baumeister40 • updated 8.0 years ago by James W. MacDonald52k

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