User: Naomi Altman

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Naomi Altman6.0k
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Posts by Naomi Altman

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Comment: C: GWAS with family data
... Thanks, Stephanie. This was actually to demonstrate GWAS to my course. The only GWAS analysis I had done previously had no family info - most of the folks I talk with have nuclear families. So even if the association is bogus, I am glad you did it this way - it brought up a number of issues I was ...
written 3.6 years ago by Naomi Altman6.0k
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Comment: C: GWASdata
... Thanks, Stephanie. I am not sure how often things gets updated, but a statement to this effect in the GWASdata documentation would be useful. I am just using the data to learn how to use GWAStools, as well. But using both sets of data together seemed "obvious" and that is how I ran into trouble. ...
written 3.6 years ago by Naomi Altman6.0k
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GWAS with family data
... Is there software in R for doing GWAS analysis with family case- control data? I started with the data in GWASdata. This is a set of 13 families of 2 ethnicities. So just treating the data as a bunch of 2x3 tables is clearly not correct. I cannot seem to find any software that is extensible. Th ...
written 3.6 years ago by Naomi Altman6.0k • updated 3.6 years ago by Paul Geeleher1.3k
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Answer: A: GWASdata
... This did not seem to go through the first time. --Naomi -------- Original Message -------- Subject: GWASdata Date: Mon, 14 Apr 2014 14:15:54 -0400 From: Naomi Altman To: Bioconductor mailing list I have been trying out some of the SNP tools using the GWASdata data sets. One th ...
written 3.6 years ago by Naomi Altman6.0k
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GWASdata
... I have been trying out some of the SNP tools using the GWASdata data sets. One thing I did was to look for differences in genotype calls between the Affy and Illumina data for what appear to be the same subjects (they have the same subject and family id). They are highly discrepant. At first I th ...
snp affy written 3.6 years ago by Naomi Altman6.0k
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Comment: C: biocLite installing to tmp directory
... Thanks for this explanation Jim. However, subsequently when I try to load the libraries they appear not to be available. (My .libPaths() looks fine.) --Naomi On 4/9/2014 12:17 PM, James W. MacDonald wrote: > Hi Naomi, > > On Wednesday, April 09, 2014 12:07:11 PM, NAOMI S ALTMAN wrote: ...
written 3.6 years ago by Naomi Altman6.0k
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biocLite installing to tmp directory
... biocLite is installing to a tmp directory instead of my (writeable) R library directory. I can fix this using "destdir" but when I am prompted for updates to other libraries, these are still being installed in tmp. This behavior appears to have started when I started using RStudio, but perhaps thi ...
written 3.6 years ago by Naomi Altman6.0k • updated 3.6 years ago by James W. MacDonald45k
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Comment: C: DiffBind counts
... Hi All, I am still trying to understand DiffBind. After reading in my data, I find that the peaks component looks something like this: head(myCHIP$peaks[[1]]) V1 V2 V3 V8 1 chr19 3182597 3183033 0.10326322 2 chr19 3589475 3589990 0.09515837 3 chr19 3831795 3832326 0.0620894 ...
written 3.6 years ago by Naomi Altman6.0k
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DiffBind counts
... I am trying to understand what DiffBind is doing. Notice that I executed exactly the same command on the same data twice and got different counts. counts=dba.count(mydata,minOverlap=3,score="DBA_SCORE_READS", bRemoveDuplicates=TRUE, bCorPlot=FALSE) head(counts$peaks[[1]]) Chr Start End S ...
diffbind written 3.6 years ago by Naomi Altman6.0k • updated 3.6 years ago by Rory Stark2.1k
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matching Entrez-IDs to Affy probesets using biomaRt
... After my premature posting yesterday, I am bit hesitant to ask, but I am puzzled by what I am getting from biomaRt. (To avoid clutter, I added the sessionInfo at the end of the message.) I used ReadAffy() to read in a rat dataset and called it CELdata. CELdata AffyBatch object size of arrays=834x ...
biomart written 3.7 years ago by Naomi Altman6.0k • updated 3.7 years ago by Marc Carlson7.2k

Latest awards to Naomi Altman

Popular Question 3.6 years ago, created a question with more than 1,000 views. For unable to install biocLite or BiocInstaller
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: limma for spectral counts
Centurion 3.6 years ago, created 100 posts.

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