User: Bandyopadhyay, Somnath Som

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Posts by Bandyopadhyay, Somnath Som

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Background correction and normalization for very small customized arrays
... Hi, I am trying to analyze gene expression data from some customized single channel arrays having only 40 genes including control probes. I have enough replicates to work with. Can anybody suggest a method for background correction and normalization for these kind of arrays? I have around 8 slides.E ...
normalization background correction written 12.1 years ago by Bandyopadhyay, Somnath Som60 • updated 4.6 years ago by Gordon Smyth39k
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Comment: C: Package "graph": bug in function addEdge
... Hi, I am trying to analyze 2 channel data without dye swap from Brucella arrays. Is there a module/package specific for the qualit control analysis of this kind of data from Brucella? -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.eth ...
written 12.6 years ago by Bandyopadhyay, Somnath Som60
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arrayQuality: error from maQualityPlots
... Hello, I am working on gene-pix two-channel data and trying to do some qc on my chips using the arrayQuality package. The following is the error message I am getting: > maQualityPlots(data) [1] FALSE Error in plot.window(xlim, ylim, log, asp, ...) : need finite 'ylim' values In additio ...
arrayquality written 12.7 years ago by Bandyopadhyay, Somnath Som60 • updated 4.6 years ago by Gordon Smyth39k
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limma: get list of genes after classifyTestsF
... I am using limma to analyze affy data. i made some contrasts and using classifyTestsF(object,p.value=0.01) I get the following results: E.OvsC.O I.OvsC.O IM.OvsC.O E.TvsC.T I.TvsC.T IM.TvsC.T C.TvsC.O E.TvsE.O IM.TvsIM.O M.TvsM.O -1 34 229 798 369 469 430 26 ...
limma classifytestsf written 12.8 years ago by Bandyopadhyay, Somnath Som60 • updated 4.6 years ago by Gordon Smyth39k
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extract info from limma results
... Hello, I am trying to use limma to analyze data from a microarray experiment. This is what I got from the contrasts I am interested in. > summary(results) P.SvsA.S P.TvsA.T P.SvsP.T A.SvsA.T -1 817 0 651 39 0 43637 45101 43724 45 ...
limma written 12.8 years ago by Bandyopadhyay, Somnath Som60 • updated 4.6 years ago by Gordon Smyth39k
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is there a way to create RLE and NUSE plots on data from txt files?
... -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of bioconductor-request at stat.math.ethz.ch Sent: Tuesday, November 07, 2006 12:43 PM To: Bandyopadhyay, Somnath (Som) Subject: Welcome to the "Bioconductor" mailin ...
written 13.0 years ago by Bandyopadhyay, Somnath Som60

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Popular Question 12.1 years ago, created a question with more than 1,000 views. For extract info from limma results

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