User: David K Pritchard
David K Pritchard • 70
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- Last seen:
- 9 years, 2 months ago
- Joined:
- 15 years, 4 months ago
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- d******@u.washington.edu
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 9.2 years ago by
David K Pritchard • 70
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... 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 9.9 years ago by
David K Pritchard • 70
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... 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 ...
written 12.5 years ago by
David K Pritchard • 70
• updated
12.5 years ago by
Amy Mikhail • 460
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... 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 ...
written 12.8 years ago by
David K Pritchard • 70
• updated
12.8 years ago by
Sean Davis ♦ 21k
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... 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 14.7 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 14.8 years ago by
David K Pritchard • 70
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... I was wondering if anyone has produced bioconductor annotation
packages for Agilent microarrays yet?
David Pritchard ...
written 15.4 years ago by
David K Pritchard • 70
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