User: colaneri

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colaneri30
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Posts by colaneri

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Testing Interactions without an interaction term in the design formula
... Hi Michael, thanks for the suggestion. Would be to much to ask short answer for my last question? Just a "no no no no "or "yes yes no yes" etc will be enough Is res1 = [3] "genotypeWT.t"?? [4] "genotypeMut.t" = res2 [2] "genotypeWTvs_Mut" = is res3? or is equal to and avarage of res3 and res4? Doe ...
written 16 days ago by colaneri30
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Comment: C: Testing Interactions without an interaction term in the design formula
... I ran the design with an interaction term: dds <- DESeqDataSet(se, design= ~genotype + genotype:condition) And I got this results: resultsNames(dds) [1] "Intercept" [2] "genotype_WT_vs_Mut" [3] "genotypeWT.t" [4] "genotypeMut.t" Comparing this approach with t ...
written 16 days ago by colaneri30
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Comment: C: Error when creating a DESeqDataSet object
... Thank you Michael Problem solved! ...
written 16 days ago by colaneri30
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Testing Interactions without an interaction term in the design formula
... I have this simple question: **how a gene modifies the transcriptional response of an organism to a treatment?** I collected RNAseq data for a wildtype (WT) and a mutant (Mut) under treatment (t) or no-treatment (u). Factor Level 1 Level 2 Genotype WT Mut Condition t u In the 4/ ...
deseq2 interactions written 17 days ago by colaneri30 • updated 16 days ago by Michael Love23k
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Error when creating a DESeqDataSet object
... Hi I have a RNAseq experiment with 2 genotypes (Wt vs Mut) and 2 conditions (treat untreat) I like to run a interaction test and I created the dds object with the below command: dds <- DESeqDataSet(se, design= ~genotype + genotype:treatment) However I got the below error, which I was tr ...
deseq2 deseqdataset written 17 days ago by colaneri30 • updated 17 days ago by Michael Love23k
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Answer: A: How to produce a dataframe with unique ENTREZID to use in gage?
... Right & thank for the clarification! I am still trying to produce a dataframe with uniquely mapped pairs of IDs (e.g  ENSEMBL -> ENTREZID or SYMBOL -> ENTREZID) Can you tell me why such a different results using two different databases? and which one you will use to go to gage-pathview? ...
written 14 months ago by colaneri30
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How to produce a dataframe with unique ENTREZID to use in gage?
... Hi I have a dataframe of reads-counts (CNTS) with 47,540 unique ENSEMBL IDs. Now I want to use gage to test for differences in gene expression over gene-sets (e.g KEGG pathways) For example: SIG.keeg.p <- gage(CNTS, gsets=kegg.sig, ref= ref.idx, samp = samp.idx, compare = "as.group") To use ga ...
annotationdbi gage ensembl entrez written 14 months ago by colaneri30
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Answer: A: Error when installing package gageData
... Dear Luo Thanks for the answer, I have also noticed what you are saying but unfortunately that is what got after running the installation of gageData this is what I got once I run: biocLite("gageData") I did install other packages (like gage in self) today and I have not problem. Any idea?     ...
written 14 months ago by colaneri30
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Error when installing package gageData
... Hi I am trying to install the gage data package from bioconductor:   source("https://bioconductor.org/biocLite.R") biocLite("gageData") However I got this error during installation (see below). I have not idea how to solve this problem. Any suggestion? ALe ##################################### ...
gage kegg written 14 months ago by colaneri30
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How to update the list of genes mapped to GO terms in the topGO object?
... I understand that the annFUN function compiles the GO terms and map genes to those terms. However when I checked the number of genes annotated for a particular GO term in my topGO object, and I compared it  with the AMIGO2 database, I noticed a big difference. For example GO:0045665 have 82 genes i ...
go topgo written 2.1 years ago by colaneri30

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Popular Question 24 months ago, created a question with more than 1,000 views. For Error: could not find function "rlog"
Popular Question 24 months ago, created a question with more than 1,000 views. For How to install S4Vector package in R v 3.1.1?

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