User: Johan Lindberg

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Posts by Johan Lindberg

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how to fastest go from Affymetrix HGU-133 Plus 2.0 chip tiff files to cel files?
... Dear all, I got Affymetrix HGU-133 Plus 2.0 chip tiff-files from a colleague, but since I want cel-files to load into R how do I extract the probe intensities in the least tedious way? Should I download the software suite from affymetrix or is there some faster way to do this? best regards, // Jo ...
probe written 11.3 years ago by Johan Lindberg270 • updated 11.3 years ago by Henrik Bengtsson2.4k
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discrepancy between limma and samr due to difference in fdr adjustment?
... Hi Mark, thanks for the reply. > 1. Does samr produce an unadjusted P-value. If so, are these > unadjusted P-vals comparable in magnitude to those from limma? an xy > plot using log="xy" might be a good way of looking at this. If they > are comparable in magnitude, then its definitely ...
limma written 11.3 years ago by Johan Lindberg270
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Comment: A: discrepancy between limma and samr due to difference in fdr adjustment?
... Dear all, I noticed that the attachments are stripped off in the mailing list so I posted them on http://picasaweb.google.co.uk/hurrayarray/FDRDiscrepancy best regards, // Johan ...
written 11.3 years ago by Johan Lindberg270 • updated 4.8 years ago by Gordon Smyth39k
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discrepancy between limma and samr due to difference in fdr adjustment?
... Dear all. I have used Limma to analyse my data and I got no differentially expressed genes correcting with multiple testing using fdr. Then a colleague of mine analysed the data and used samr, the package by the guys from Stanford, http://www-stat.stanford.edu/~tibs/SAM/ and got ~600 genes with an ...
limma written 11.3 years ago by Johan Lindberg270
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error when using GOstats with AnnBuilder built package
... Dear All, has there been a change in how you build you own annotation with AnnBuilder to use with e.g. GOstats? I just reannotated our in-house spotted human oligo chip and got an error message when using GOstats. > hgOverCond <- hyperGTest(params) Error in do.call(paste(pname, "dbconn", se ...
annotation go gostats oligo written 11.4 years ago by Johan Lindberg270 • updated 11.4 years ago by Marc Carlson7.2k
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gene expression using biopsies/mixtures of cell lines
... Dear all, Im sorry if this is a question not directly related to using bioconductor packages, but at least I used them for the analysis that I need a reference to ;o) I have a biopsy related project with 63 unpaired biopsies in total and two groups where I cannot find any differences using limma, ...
limma written 11.4 years ago by Johan Lindberg270
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ABPkgBuilder trouble
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080131/ 6bf3c9aa/attachment.pl ...
written 11.8 years ago by Johan Lindberg270
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Comment: C: ABPkgBuilder trouble
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070306/ 5a69b41c/attachment.pl ...
written 12.7 years ago by Johan Lindberg270
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Comment: C: ABPkgBuilder trouble
... Thank you for your help Nianhua. Its greatly appreciated. I followed your instructions and everything went according to plan except for that the script didn't write anything to myoutput.txt (its empty). So I guess this is were the problem resides, but i have no idea what to do about it. Any suggest ...
written 12.7 years ago by Johan Lindberg270
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ABPkgBuilder trouble
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070305/ 78afc3d5/attachment.pl ...
written 12.7 years ago by Johan Lindberg270 • updated 12.7 years ago by Nianhua Li870

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