User: Louisa A Rispoli/AS/EXP/UTIA

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Posts by Louisa A Rispoli/AS/EXP/UTIA

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Comment: C: probesets from a KEGGHyperGParams instance
... Jim- Thank you for the prompt reply. I am using affy ids and performing the analysis similar to your description. I was just trying to figure out if there was a way to append the htmlReport to include the geneIDsByCategory or affy probes without making my head or computer explode. Thank you again f ...
written 11.0 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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probesets from a KEGGHyperGParams instance
... To anyone with a lot more experience. I have been trying to read through all the helps and vignettes for a simple way to get the probesets that went into producing significance of KEGG term after running hypergeometric test for KEGG. I have found probeSetSummary for GO terms and hyperGoutput (also ...
go written 11.0 years ago by Louisa A Rispoli/AS/EXP/UTIA160 • updated 11.0 years ago by James W. MacDonald51k
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Background values
... Hi all- I have been doing our microarray analysis looking at the QC metrics provided by SimpleAffy and releazed that all the data produced is based on the MAS5.0 algorithm. I was wondering if there was any way to get qc metrics if use RMA or GCRMA, specifically we want to know about the background ...
microarray gcrma simpleaffy written 11.2 years ago by Louisa A Rispoli/AS/EXP/UTIA160 • updated 11.2 years ago by Wolfgang Huber13k
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siggenes failure
... To all- I have finally figured out how to use ebam and incorparate a database so I can know what genes are interesting, or at least it was working yesterday but no longer. For some reason the ebam is not the right S4 object though I am using the same code as I did yesterday. I can not figure out w ...
go written 11.3 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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Comment: C: bovine Annotation package(s)
... Hi Nathan- I would greatly appreciate it if you could send the package. A grad student trying to finish her PhD and I are trying to understand annotation so we can apply to the gene lists we finally figured out how to do our linear model, ebayes and fdr on. We are really frustrated since most packa ...
written 11.3 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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Comment: C: bovine Annotation package(s)
... Marc- I was wondering how it was going with building a bovine annotation database? I have been reading through the vignette for AnnBuilder and not sure that I have the skills for building the bovine. Is there something else that I need to be reading to assist? Thanks Louisa Rispoli "If we knew ...
written 11.3 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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RMySQL
... Hi all- In effort to follow vignettes I have run into an package issue. I have been trying to understand the latest posts on errors in the RMySQL for Windows package. And I think my lack of knowledge in the computer language department is rising up an keeping me from solving the problem. As far a ...
go written 11.3 years ago by Louisa A Rispoli/AS/EXP/UTIA160 • updated 11.3 years ago by alex lam RI30
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siggenes and permutations
... Hi all- We are investigating SAM and EBAM analysis for our data and run into a problem that reading the archives has not helped any. We performed SAM on a data set and noticed the permutations randomly selected 100 to generate the results. We were curious what that meant and if had anything simila ...
go written 11.4 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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Comment: C: Understanding limma, fdr and topTable
... Jim, Tom and Naomi and all- Thank you for your reponses. I am planning to look for genes (if any) that changed similaryly between the two groups depending on amplification procedure but was just getting starting looking at individually first. I appreciate the advice. Would pre-filtering to remove " ...
written 11.4 years ago by Louisa A Rispoli/AS/EXP/UTIA160
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Understanding limma, fdr and topTable
... To all- I am a newbie trying to analyze microarray with minimal help and thought that I had figured out all. We have a simple task of comparing two groups with 8 replicates on the bovine genechip. I am attempting to understand the results that I obtain using limma and adjusting for fdr. I have tri ...
microarray go limma written 11.4 years ago by Louisa A Rispoli/AS/EXP/UTIA160 • updated 11.4 years ago by Robson, Samuel10

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Popular Question 11.0 years ago, created a question with more than 1,000 views. For Understanding limma, fdr and topTable

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