User: Naomi Altman

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Naomi Altman6.0k
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Posts by Naomi Altman

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Answer: A: biomaRt and rma
... It seems like a given that as soon as I send a message to the list, the problem corrects itself. --Naomi ...
written 5.7 years ago by Naomi Altman6.0k
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biomaRt and rma
... I have been trying to use biomaRt to get entrezIDs for my Affymetrix probesets. This works fine, but is not what I want: library(affy) CELdata=ReadAffy(celfile.path=celfileDir) features=featureNames(CELdata) library(biomaRt) ensembl = useMart("ensembl",dataset="rnorvegicus_gene_ensembl") getBM(at ...
biomart written 5.7 years ago by Naomi Altman6.0k • updated 5.7 years ago by James W. MacDonald52k
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Comment: C: unable to install biocLite or BiocInstaller
... Thanks everyone. You are undoubtedly correct as I did not have problems with installation on my personal laptop. I will talk with the local IT folks about the set-up at work. --Naomi > Hi, > > On Tue, Jan 14, 2014 at 10:04 AM, Vincent Carey > wrote: >> my conjecture is that ...
written 5.8 years ago by Naomi Altman6.0k
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unable to install biocLite or BiocInstaller
... sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages ...
written 5.9 years ago by Naomi Altman6.0k • updated 4.1 years ago by av0
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Comment: C: technical + biological replicate design for multiple categories
... The blocking variable can have text. Your treatment variable is now correct and as far as I can see, your analysis should now be fine. --Naomi At 05:34 PM 7/3/2013, you wrote: >On Jul 3, 2013, at 1:32 PM, Naomi Altman wrote: > > > You need to have a variable "biorep" with biorep num ...
written 6.4 years ago by Naomi Altman6.0k
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Answer: A: What is the FDR set to for the BH method.
... The "adjusted p-value" for the i_th smallest p-value is mp/i if this is less than 1 and greater than the "adjusted p-value" for the (i-1) smallest p-value. It is truncated at 1.0 from above and at the value for the (i-1) value below (so that it always increases as p increases). This is the estima ...
written 6.4 years ago by Naomi Altman6.0k
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Answer: A: technical + biological replicate design for multiple categories
... You need to have a variable "biorep" with biorep number e.g. c(1,1,2,2,3,3,...6,6) This is a blocking variable. The treatments are just Cyt1, Cyt2 and Mock. You will need to follow the instructions for blocking variables. --Naomi At 05:15 PM 7/2/2013, James Platt wrote: >I am using Limma fo ...
written 6.4 years ago by Naomi Altman6.0k
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Comment: C: edgeR multiple contrasts Vs. One test
... What method is used for FDR control in exactTest? Thanks, Naomi ...
written 6.4 years ago by Naomi Altman6.0k • updated 23 months ago by Gordon Smyth39k
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Answer: A: Different number of differentially expressed genes after using ComBat in 'sva' f
... There are several possibilities about why this happened, but one is power. Limma (and all ANOVA routines) uses the MSE computed from all the groups to determine differences among groups. Since Batch 2 is very small, you did not have a good measure of MSE in the analysis that included only Batch 2. ...
written 6.4 years ago by Naomi Altman6.0k
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qvalue pi0 computation
... I just updated R and Bioconductor and reran an analysis. In particular qvalue(p)$pi0 is giving me really different answers than the last time I ran it (same p) about a year ago. Any hints as to why would be most appreciated. Session info is below for the current session. I do not have the info ...
written 6.8 years ago by Naomi Altman6.0k • updated 6.8 years ago by James W. MacDonald52k

Latest awards to Naomi Altman

Popular Question 5.6 years ago, created a question with more than 1,000 views. For unable to install biocLite or BiocInstaller
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: limma for spectral counts
Centurion 5.6 years ago, created 100 posts.

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