User: Seungwoo Hwang

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9 years, 1 month ago
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12 years ago
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Posts by Seungwoo Hwang

<prev • 8 results • page 1 of 1 • next >
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Obtaining unadjusted permutation p-value from GeneMeta package
... Dear all, I have a question on GeneMeta package (release 2.7). The GeneMeta vignette shows how to obtain FDR by zScoreFDR() function, but it does not show how to obtain unadjusted p-value which is estimated from randomly permuted z-score distribution. I know that the zScoreFDR() function involves ...
genemeta written 9.1 years ago by Seungwoo Hwang80
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Are individual channels' intensities comparable across cDNA arrays?
... Dear all, I received the following request. I'm not so sure about it and I would like to receive your expert opinion on this. The platform is cDNA array with two experimental series. - On series 1 chips, tumor sample from a patient (Cy5) and normal sample from pooled healthy individuals (Cy3) were ...
normalization limma written 11.1 years ago by Seungwoo Hwang80 • updated 11.1 years ago by Sean Davis21k
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Data consisting of several groups, persons, and cells
... Dear all, I have a question on how to analyze the following Affymetrix gene expression data. - There are three groups (each representing a haplotype). - There are several persons in each group (3 persons in group 1, 5 persons in group 2, and 4 persons in group 3). - There are 4 biological replicate ...
written 11.2 years ago by Seungwoo Hwang80
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Two cDNA arrays whose samples are the same but probes are not
... Dear all, I am struggling with dealing with an unusual cDNA microarray data which were generated long time ago by a lab next door. Their platform was 24K cDNA array. In order to enlarge genome coverage, they prepared two probe libraries and printed them onto two arrays. Let's call them array A and ...
microarray probe written 11.3 years ago by Seungwoo Hwang80
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Filtering probes without annotation prior to statistical test
... Dear all, I am analyzing data from Affymetrix Human Gene 1.0 ST Array. After inspecting its probe annotation file, it came to my attention that it contains a lot of probesets without transcript annotation as follows; Total number of probesets: 33,298 (1) Probesets with annotation: 24,409 (73%) (2 ...
annotation probe written 11.4 years ago by Seungwoo Hwang80 • updated 11.4 years ago by Mark Cowley910
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Cutoff to use for IQR filtering in genefilter
... I am wondering what cutoff value I should use for IQR filtering in genefilter. I did some literature search. It varies from paper to paper. I have read two papers so far. One used 0.5, the other used 0.18. affylmGUI has an option of 0.5, 0.25, and 0.1. I also searched Bioconductor archive and read ...
affylmgui written 11.5 years ago by Seungwoo Hwang80 • updated 11.5 years ago by Mark Cowley400
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How to input three datasets into OrderedList package
... After reading OrderedList user's guide, it seems to me that the package allows only two sets of expression data or two lists. However I have three datasets and three lists. Is there any way that I can do meta-analysis of three of them altogether using OrderedList package? Thanks, Seungwoo ------- ...
orderedlist written 11.8 years ago by Seungwoo Hwang80 • updated 11.8 years ago by Sean Davis21k
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Applying separate normalization methods to replicate arrays
... I have a conceptual question on normalization of replicate arrays. Let's say I have several replicate arrays. I wonder whether it is advisable or not to apply different normalization methods to each of the replicate arrays. Let me illustrate with the following two situations. (1) By inspecting the ...
normalization written 12.0 years ago by Seungwoo Hwang80 • updated 12.0 years ago by Sean Davis21k

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Popular Question 9.1 years ago, created a question with more than 1,000 views. For Cutoff to use for IQR filtering in genefilter

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