User: alex lam RI

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alex lam RI310
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Posts by alex lam RI

<prev • 31 results • page 1 of 4 • next >
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Understanding GOstats
... Dear colleagues, I would like to check if my understanding onone aspect of GOstats is correct. The probeset 1370428_x_at is linked to the GO term GO:0002474 When I use hyperGTest (with conditional=F), if this probeset is DE, enrichment of GO:0002474 will be tested. And so will its parent GO term ...
annotation go affy gostats written 11.7 years ago by alex lam RI310 • updated 11.7 years ago by James W. MacDonald52k
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How to get affyId from GOstats output
... Dear colleagues, After running hyperGTest, summary(hgOver) returns a table of GO IDs, Pvalues, Count ...etc For example, for a particular GO term the Count = 3 and Size = 9. How do I retrieve the affyIDs of those 3 and 9 genes? Many thanks, Alex > sessionInfo() R version 2.6.1 (2007-11-26) i3 ...
go rae230a written 11.7 years ago by alex lam RI310 • updated 11.7 years ago by James W. MacDonald52k
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Control probe
... Dear users, Are all control probesets on affy chips suppose to be house-keeping (express to a certain extent?) The AFFX_rat_5s_rRNA probeset on my dataset (rat 230a arrays) seems to have extremely low intensity across all samples (around 1.3 after gcrma), I wonder if this is normal? Many thanks, A ...
affy written 11.9 years ago by alex lam RI310
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Answer: A: sample size estimation in genome wide association studies / packages
... Hi PingZhao, Are there any papers describing Quanto? And does it work with quantitative traits? Thanks, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guar ...
written 11.9 years ago by alex lam RI310
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Answer: A: Storey and Tibshirani FDR
... Hi Daniel, Storey's group released a package in CRAN called qvalue. Cheers, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotlan ...
written 11.9 years ago by alex lam RI310
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Answer: A: sample size estimation in genome wide association studies / packages
... Hi Phillipe, You mean how many samples you need in a case-control GWA? If yes, read this article: Genome-wide association studies: theoretical and practical concerns. Wang WY, Barratt BJ, Clayton DG, Todd JA. Nat Rev Genet. 2005 Feb;6(2):109-18. Alex -------------------------------------------- ...
written 11.9 years ago by alex lam RI310
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Comment: C: minimum expression level (Simpleaffy)
... Hi Patricia, The exprs() function will return a matrix of expression values, with rows being probesets, and columns being samples. For example you can get the mean expression value for each probeset like this: apply(exprs(your.eset.object), 1, mean) This will give you one value per probeset. Then ...
written 11.9 years ago by alex lam RI310
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Answer: A: minimum expression level (Simpleaffy)
... Hi Patricia, Between 2.15 - 14.6 sounds about right. Remember the intensities are in log scale after GCRMA or RMA. In my last affymetrix analysis I think I used ~ 3.5. It was decided in an ad-hoc way by looking at the distributions: those under this threshold in my dataset also had very low variabi ...
written 11.9 years ago by alex lam RI310
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MBNI CDF
... Dear BioC users, I am going to use the custom CDF released by MBNI for the array rae230a. Does anyone know of any methods / webpage for getting basic statistics such as how many probesets did not match ensembl, how many probes were removed because of SNPs ... etc? Many thanks, Alex --------------- ...
cdf written 11.9 years ago by alex lam RI310 • updated 11.9 years ago by James W. MacDonald52k
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Comment: C: Disorderly duplicate spots
... Dear Patricia, Please do not hijack a thread and ask a different question to the subject line. How many genes depends on your arrays quality and the biology of your experiment. There will be some genes that are silent across all of the conditions. Why don't you plot the mean expression and varianc ...
written 11.9 years ago by alex lam RI310

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