User: Loren Engrav

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Loren Engrav1.0k
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Posts by Loren Engrav

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Answer: A: Affy PA calls
... Ok, sounds as if p and q trump PA calls I will cease and desist on thinking to use PA calls after p and q to further refine things Thank you all > From: Mark Cowley > Date: Fri, 30 Jul 2010 13:43:59 +1000 > To: Loren Engrav > Subject: Re: [BioC] Affy PA calls > > no worries. ...
written 8.9 years ago by Loren Engrav1.0k
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Comment: C: Affy PA calls
... Thank you both Will try to explain better Have Affy chips from shallow and deep wounds in 3 Duroc and 3 Yorkshire pigs Prior to maanova and q-value I did strip all probes that were Absent on all 60 chips Now then with maanova and q-value I have 171 probes of statistical interest, but In this se ...
written 8.9 years ago by Loren Engrav1.0k
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Comment: C: Affy PA calls
... Sorry if was too terse I have Affy chips from shallow and deep wounds in 3 Duroc and 3 Yorkshire pigs. And I have the p-values from maanova and q-values from Storey q-values which returned 171 probes of interest. I would also like the 3 Durocs and the 3 Yorkshire bio reps to be the "same". So th ...
written 8.9 years ago by Loren Engrav1.0k
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Affy PA calls
... Does anyone put much stock in Affy PA calls? I searched gmane and I think the answer is No. True? Thank you. ...
affy written 8.9 years ago by Loren Engrav1.0k
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Comment: C: Romer and symbols2indices query
... Thank you By pdfs I meant the limma documentation pdfs But I downloaded the C2 file and will use same In fact I might run the homemade file against the rdata file and see how they compare as well Thank you again > From: Gordon K Smyth > Date: Fri, 7 May 2010 10:51:52 +1000 (AUS Eastern S ...
written 9.1 years ago by Loren Engrav1.0k
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Answer: A: Romer warning serious? and nrot=9999?
... Thank you Small data set? Yes, my data set is small, 1842 genes of interest at week1 2 3 12 or 20 between Duroc and Yorkshire breeds after filters And the warning occurs only for week1 where the differential is the smallest of all 5 time points with only a handful of differentially expressed genes ...
written 9.1 years ago by Loren Engrav1.0k
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Comment: C: Romer and symbols2indices query
... Thank you very much, this is interesting I did as you suggest and 7 of 1842 symbols were "incorrect" I will fix and rerun Thank you again, am grateful > From: Gordon K Smyth > Date: Fri, 7 May 2010 10:35:55 +1000 (AUS Eastern Standard Time) > To: Loren Engrav > Cc: Yifang Hu , rb ...
written 9.1 years ago by Loren Engrav1.0k
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Answer: A: Romer and symbols2indices query
... Thank you for the response Well maybe I don't, and maybe I shouldn't. My thought was that tomorrow or day after or ??? there will be a new version of the .gmt file and it would be useful to just be able to quickly rerun things. But maybe that is faulty logic, maybe the .gmt files do not change th ...
written 9.1 years ago by Loren Engrav1.0k
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Romer warning serious? and nrot=9999?
... So ran romer with romer(iset, y, design, contrast, array.weights=NULL, block=NULL, correlation, floor=FALSE, nrot=9999) Finished with no errors but I see Warning In romer (iset, y, design, : Estimation of var.prior failed ­ set to default value romer2 finished with same message Am I in trouble? ...
written 9.1 years ago by Loren Engrav1.0k
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Comment: C: Romer and symbols2indices query
... Bingo, thank you and romer ran These missing little tidbits can be brutal > From: Martin Morgan > Date: Wed, 05 May 2010 05:11:02 -0700 > To: Loren Engrav > Cc: rbioc > Subject: Re: [BioC] Romer and symbols2indices query > > On 05/04/2010 07:57 PM, Loren Engrav wrote: > ...
written 9.1 years ago by Loren Engrav1.0k

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