User: David K Pritchard

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Posts by David K Pritchard

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Comment: C: hclust for 13000 genes
... Avhena, I would recommend that you not use R for this application. For hierarchical clustering of large numbers of genes + visualization I would recommend you try the free MeV program that can handle 20,000 genes easily. David On Wed, 17 Mar 2010, avehna wrote: > Hi again, > > I'm ...
written 9.0 years ago by David K Pritchard • 70
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Answer: A: R: Found seven 3'UTR sequences attributed to the same ensembl_gene_id
... Maura, many genes can make multiple transcripts with different structures that we call alternative spliceforms. It is quite possible to have a gene which has multiple transcripts with 7 different 3'UTRs. A good place to check this out is the ensembl website that will show you the structure of t ...
written 9.7 years ago by David K Pritchard • 70
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Some Genefilter questions
... Robert, there are two sets of studies which have suggested the ~ 40% expression level from what I remember. Classic COT curve studies from several decades ago suggested roughly this level. More recently, MPSS (Massive Parrelel Signature Sequencing) studies have also suggested this is a reasona ...
normalization survival cancer cdf genefilter geneplotter affy affydata widgettools gcrma written 12.3 years ago by David K Pritchard • 70 • updated 12.3 years ago by Amy Mikhail • 460
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Microarray analysis with continuous variables
... We are currently working on a microarray project where we have to correlate both clinical and morphological (MRI) data with human expression data. Much of the data is in the form of continuous variables. While it can be turned into the categorical classifications most often used in array analy ...
microarray written 12.6 years ago by David K Pritchard • 70 • updated 12.6 years ago by Sean Davis ♦ 21k
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Answer: A: Re: [S] Error in clustering procedure
... Christian, I think it is overstating the matter to say it is useless to hierarchically cluster 7000 genes. In most studies where one is comparing only a two or a few different conditions there is generally not alot of structure in the data and clustering is not useful. However, I have been invo ...
written 14.6 years ago by David K Pritchard • 70
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Comment: C: Harsh results using limma!
... I think Mick's experiences point out a fundamental problem with current statistical analysis of microarray data. If his data was .2, .2, .2, (dye flips) -.2, -.2, -.2 then Limma would note this gene as highly differentially expressed. In contrast when he sees 6.29, 5.54, 0.2, (dye flips)-5.27,-4 ...
written 14.6 years ago by David K Pritchard • 70
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Annotation data packages for Agilent arrays?
... I was wondering if anyone has produced bioconductor annotation packages for Agilent microarrays yet? David Pritchard ...
written 15.2 years ago by David K Pritchard • 70

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