User: Michal Blazejczyk

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Posts by Michal Blazejczyk

<prev • 32 results • page 1 of 4 • next >
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Problems with VST in lumi
... Hi, We are creating lumiBatch objects manually the following way, using matrices of data: if( !exists( "controlData" ) ) controlData <- data.frame() if( !use.beadCounts ) beadCount <- new( "matrix" ) # otherwise the object already exists if( !use.detPValues ) detectionPValue <- new ...
written 8.7 years ago by Michal Blazejczyk320
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Answer: A: Human Gene 1.1 ST cdf
... Hi Nicolas, There was a thread here about two weeks ago that discussed this specific question. The question was: > I have noticed that Bioconductor's just.rma() function returns fewer transcript-level > probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probeset ...
written 8.7 years ago by Michal Blazejczyk320
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Answer: A: RMA in Bioconductor versus APT - missing probesets
... Dear Mark, Thank you for your answer. Please correct me if I'm getting the wrong impression, but doesn't this mean that just.rma() and rma() are simply wrong in this case? And if that's the case then should they be used for ST data? In previous versions of Biocionductor they simply did not work ...
written 8.8 years ago by Michal Blazejczyk320
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Comment: C: RMA in Bioconductor versus APT - missing probesets
... Dear Christian, I am aware of the existence of xps. However, we can't use it for our purposes, largely because it is too complicated to set up (or at least, that was the case the last time we looked at it). I would still like to know what's happening in just.rma() :) Best, Micha? cstrato wr ...
written 8.8 years ago by Michal Blazejczyk320
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RMA in Bioconductor versus APT - missing probesets
... Dear group, I have noticed that Bioconductor's just.rma() function returns fewer transcript-level probesets that RMA in APT for the Human Gene 1.0 ST array. To be specific, 819 probesets are missing, and most of them seem to be "real", i.e. they are annotated when I run them through NetAffx. I wo ...
written 8.8 years ago by Michal Blazejczyk320 • updated 8.8 years ago by cstrato3.9k
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affy package and ST arrays
... Dear list, I have a question. I've noticed that The most recent Biocinductor version contains CDF packages for Affymetrix's ST arrays. As a result, functions such as rma() or just.rma() now work well with these arrays, which is great. However, many other normalization functions (e.g. gcrma(), ma ...
normalization cdf written 9.0 years ago by Michal Blazejczyk320 • updated 9.0 years ago by cstrato3.9k
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Combining Affymetrix miRNA samples from different arrays
... Dear group, We have a customer who has two datasets obtained using two Affymetrix miRNA arrays: miRNA-1_0 and miRNA-1_0_2xgain. The data are supposed to be analyzed together but the problem is that the expression profiles from both arrays look very different. Here's what I did so far: - Normaliz ...
normalization cdf written 9.0 years ago by Michal Blazejczyk320 • updated 9.0 years ago by James W. MacDonald52k
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SAM results
... Dear List, I have a question regarding p-values, d-values and q-values returned by Bioconductor's SAM method (siggenes package). - My understanding is that the p-values returned are unadjusted. Does it make sense to apply standard FDR procedres (e.g. Benjamini- Hochberg) to them? - What i ...
written 9.1 years ago by Michal Blazejczyk320 • updated 9.1 years ago by Holger Schwender900
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Removing raw probes in affy data
... Hello everyone, Is it possible to remove certain probes before normalizing Affymetrix data? I have a client who is worried about cross-hybridization in one of his genes of interest, and he would like to remove the probes that are causing this. Best regards, Michal Blazejczyk FlexArray Lead Devel ...
written 9.1 years ago by Michal Blazejczyk320 • updated 9.1 years ago by Guido Hooiveld2.5k
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miRNA normalization using affy package?
... Hi everyone, I'm curious to hear what R packages you would recommend for the normalization of data from Affymetrix miRNA arrays? Is the standard affy package performing well? What CDF package is best to use? Best regards, Michal Blazejczyk FlexArray Lead Developer McGill University and Genome Que ...
mirna normalization cdf affy written 9.1 years ago by Michal Blazejczyk320 • updated 9.1 years ago by Guido Hooiveld2.5k

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