User: MARIA STALTERI

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Posts by MARIA STALTERI

<prev • 16 results • page 1 of 2 • next >
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Annotation for Mouse 430 2.0 and Human Genome U133 Plus 2.0 Arrays
... Hi Dorothy, The Mouse 430A 2.0, Mouse 430 2.0, and MOE430A are different arrays. As I understand it, the hgu133plus2 and hgu133plus2.db packages contained the same information, only in different formats. But only the hgu133plus2.db format appears to be included in the current release (2.3) of B ...
hgu133plus2 moe430a written 10.7 years ago by MARIA STALTERI160
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Answer: A: Affymetrix Mogene 1 0 ST
... Hi Al, I don't know about the Mouse Gene arrays, but with regard to the Human Exon arrays, I came across something in one of the Affymetrix manuals (exon_array_design_technote.pdf) that says the intron/exon control probe sets are derived from the consensus sequences of the HG-U133 Plus 2 array nor ...
written 10.8 years ago by MARIA STALTERI160
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Answer: A: Does the strand of a microarray probe matter?
... Hi Cei, I think you may still be a little confused about what the gene expression arrays are designed to measure. The probes on the Affymetrix 3' expression arrays are single-stranded oligos having the sense sequence, i.e. the same sequence as the mRNA they are designed to detect, and the IVT as ...
written 10.9 years ago by MARIA STALTERI160
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Answer: A: Does the strand of a microarray probe matter?
... Hi Cei, The Illumina BeadArrays use a variety of assays. The whole genome gene expression arrays such as the HumanWG-6 and HumanRef-8 use a 3' based assay (IVT or in-vitro transcription assay) very similar to the one used with the older 3' Affymetrix arrays. Some of the older or custom gene expr ...
written 10.9 years ago by MARIA STALTERI160
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Answer: A: Affymetrix probeset ids to gene symbols
... Hi Kurt, Jim, Affymetrix arrays such as the hg-u133b were designed to target the 600 bp at the 3' end of the transcript, not the start of the transcript. We have found that the many-to-one mappings between probesets and genes are often due to alternative splicing, use of alternative poly(A) sites ...
written 11.3 years ago by MARIA STALTERI160
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Answer: A: difference between annotation
... Hi Gregory, There are some differences between limma(bioconductor) annotations and Affymetrix annotations because bioconductor and Affymetrix use different methods to obtain the annotations. Bioconductor uses the RepresentativePublicIdentifier given by Affymetrix as the starting point for the ann ...
written 12.8 years ago by MARIA STALTERI160
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Answer: A: a question for Metadata package: hgu133a
... Hi Tao, At least in the two examples you have given, it seems that the second field is just a continuation of the gene name, or description of the gene, so it would make more sense to combine the two fields, since they refer to the same gene. If a probeset maps to more than one gene, then it wou ...
written 13.1 years ago by MARIA STALTERI160
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problem with moe430a version 1.12.0?
... Hi, Is there a problem with the latest release of the moe430a annotation package or am I having problems installing it on my computer? I am running R2.3 on Mac OSX. I downloaded the source file for the latest version of the moe430a (moe430a_1.12.0.tar.gz) and tried to install it from the R menu. ...
hgu133a hgu133plus2 moe430a moe430b rae230b probe written 13.5 years ago by MARIA STALTERI160
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Comment: C: metadata - annotation package changes
... The 1.5 packages were built in March 2004. On Wed, 10 Aug 2005, John Zhang wrote: > Date: Wed, 10 Aug 2005 09:13:17 -0400 (EDT) > From: John Zhang > To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > Cc: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at stat.mat ...
written 14.2 years ago by MARIA STALTERI160
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Comment: C: metadata - annotation package changes
... Can you remember roughly when the previous time that you extracted the accession numbers from the Affymetrix files was? I keep asking because as far as I can tell, the Affymetrix Representative Public IDs have not changed since the first version of the annotation files that I have worked with, whi ...
written 14.2 years ago by MARIA STALTERI160

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