User: Guilherme Rocha

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Posts by Guilherme Rocha

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Comment: C: edgeR vs glm.nb
... This is also a basic question but I am having a hard time finding it in the documentation. If y is a DGE list object which contains norm.factors and lib.size, are these already included in the GLM regression model or must one explicitly add them via the lib.size parameter and/or design matrix. Put ...
written 3.6 years ago by Guilherme Rocha40
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Comment: C: QC probes in HTA2-0
...   Thanks, James.   Do you know where to find documentation detailing what these control probesets are?   Also, do I understand correctly that there are probes used to both serve as control AND measure transcripts (main///normgene->exon)?    ...
written 4.0 years ago by Guilherme Rocha40
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QC probes in HTA2-0
...   Hi all,   In the simpleaffy package, there are a series of deprecated functions for picking up QC probes in microarray chips, namely:   getTao(name) getAlpha1(name) getAlpha2(name) getActin3(name) getActinM(name) getActin5(name) getGapdh3(name) getGapdhM(name) getGapdh5(name) getAllQCProbes(name ...
affy simpleaffy qc hta written 4.0 years ago by Guilherme Rocha40 • updated 4.0 years ago by James W. MacDonald49k
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Comment: C: Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
... If you are thinking of using the na34 version of the Affy probeset annotation files (".../HTA-2_0.na34.hg19.probeset.csv"), notice that in that file, 2995 probesets are identified by their NUMERICAL id whereas the remaining probesets are identified by their ALPHANUMERICAL ids. GVR   ...
written 4.0 years ago by Guilherme Rocha40
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Comment: C: Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
...   I've also had some problem using the na34 annotation file to construct the InfoPackage for HTA-2.0.   It appears that, for 2995 of the probesets,  the probeset_id column in na34 lists the numerical id of the probeset rather than its alphanumeric id. As far as I could tell, that was the source of ...
written 4.0 years ago by Guilherme Rocha40
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Comment: C: Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
... Thank you. Your reply helps a lot in letting me know where to look for things. :) Best, G On Wed, Aug 27, 2014 at 11:08 AM, James W. MacDonald wrote: > Hi Guilherme, > > > On Tue, Aug 26, 2014 at 10:00 AM, Guilherme Rocha > wrote: > >> Hi all, >> >> ...
written 4.6 years ago by Guilherme Rocha40
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Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
... Hi all, I have constructed a package information file for Affy's HTA 2.0 chip using pdInfoBuilder as shown below. It appears that the annotation files have been upgraded to na34 (from na33 in probeFile and transFile). Specific question: do the annotation files affect which probes are inclu ...
biocviews annotation organism pdinfobuilder written 4.6 years ago by Guilherme Rocha40 • updated 4.6 years ago by James W. MacDonald49k
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RMA normalization in large number of chips
... Dear all, I am trying to pre-process (bg correction, quantile normalization, summarization) the readings in a large number (~1,000s) of large microarray chips (~10^6 probes). As far as I can tell, pre-processing functions in most packages will load data from all chips at once which, in this c ...
normalization probe preprocesscore written 5.1 years ago by Guilherme Rocha40 • updated 5.1 years ago by James W. MacDonald49k
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pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
... Dear all, I am trying to create the pfInfoBuilder packages for Affy's GeneChip Human Transcriptome Array 2.0. I am using the "original" pgf, clf, mps, and probeset.csv files from the library files from Affy's website ( http://www.affymetrix.com/Auth/analysis/downloads/lf/hta/HTA-2_0 /AGCC_library ...
biocviews annotation organism oligo oligoclasses written 5.2 years ago by Guilherme Rocha40 • updated 3.9 years ago by Jason Hubbard20

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Popular Question 23 months ago, created a question with more than 1,000 views. For Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder

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