User: Jeff Sorenson

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Posts by Jeff Sorenson

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Affy and Custom CDF files
... If I create a custom CDF file in which a particular probe may be listed in more than one probe set, then will the results of the RMA algorithm in affy still be valid? Thanks, Jeff Sorenson ...
cdf probe written 14.7 years ago by Jeff Sorenson70 • updated 14.7 years ago by Rafael A. Irizarry2.3k
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Transcription factors and gene networks
... Is anyone aware of a public resource (other than pubmed) for cataloging the influence of genes on one another? Ideally, a it would be a list of coefficients for the dependence of gene transcription on the products of other genes and factors, such as d(gene(i))/dt=a(i,j)gene(j)+b(i,j,k)gene(j)gene(k ...
written 14.7 years ago by Jeff Sorenson70
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Answer: A: Reading of .DAT files using Bioconductor
... On Linux, I've been using the rawtopgm utility followed by the convert utility to obtain a file that can be viewed. > Date: Tue, 11 Feb 2003 22:37:20 -0500 > Subject: Re: [BioC] Reading of .DAT files using Bioconductor > Cc: bioconductor@stat.math.ethz.ch, Tapan Mehta > To: Laurent Gau ...
written 14.8 years ago by Jeff Sorenson70
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RE: PCA plots
... For a simple 3-D scatter plot, I've settled on a perl script that converts any three principle components (calculated by R) into a 3-D VRML scatterplot (.wrl) file that can viewed with most web browsers. The script is adapted from an online tutorial http://staff.washington.edu/larryg/Classes/Rvrml/ ...
microarray go written 14.8 years ago by Jeff Sorenson70
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RE: Bioconductor digest, Vol 1 #210 - 10 msgs
... Can anyone point me to a reference where these numbers regarding false positives were derived? This is a huge difference! Thanks, Jeff Sorenson > > two things to keep in mind: > > 1) rma return log2 expression so make > sure to use 2^(exp1-exp2) to compute fold change. > > 2) ...
written 14.8 years ago by Jeff Sorenson70
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Filtering and Multiple Testing
... Just curious .... The genefiltering package doesn't seem to account for multiple testing. We have a separate package for that: multtest. Since adjustments for multiple testing are essential, are there plans to incorporate that functionality into genefilter? Or are most people just doing their filt ...
multtest written 14.8 years ago by Jeff Sorenson70 • updated 14.8 years ago by rgentleman5.5k
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Annotation for Nonspecificity of Affymetrix Probes?
... I would like to thank all of the contributors to the bioconductor project for putting their tools into the public domain. I'm embarking on a project using Affymetrix U133A/B chips and have been in the process of setting up a database of probe/sequence information and other annotation information (m ...
probe process written 15.3 years ago by Jeff Sorenson70 • updated 15.3 years ago by rgentleman5.5k

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