## User: cagenet34

cagenet3420
Reputation:
20
Status:
New User
Location:
Toulouse, France, INRA
Last seen:
1 week, 3 days ago
Joined:
3 years, 3 months ago
Email:
c***********@inra.fr

#### Posts by cagenet34

<prev • 23 results • page 1 of 3 • next >
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... Oups..... ok that means that I need two coffee cups or need holidays....sorry again and thank you so much for your help !!   ...
written 13 months ago by cagenet3420
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... Hello James Thank you for your reply. I would like the vgnc for bovine. Thank you for your example from which I deduced that there is still no VGNC name attribute in Biomart.  ... Am I right. For the url, It was because in a first attempt I was responding to news "Ensembl 93 is out" from Amonida " ...
written 13 months ago by cagenet3420
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... Hi Gilles you can use the following packages : - AnnotationDbi -Annotate -Ensembldb -Biomart Here are the following code I used for using Bovine Ensembl DB for differential expression analysis ensembl_mart_93 <- useEnsembl(biomart="ensembl")# to use the latest ENSEMBL version mart= useM ...
written 13 months ago by cagenet3420
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... I'm using Biomart package after differential expression analysis with DESeq2 package. I used ENSEMBL ID. After differential analysis I would like to obtain the HGNC symbol or VGNC symbol from ENSEMBL ID. The following function work for HGNC symbol but I failed to retrieve vgnc gene name. add.anns ...
written 13 months ago by cagenet3420 • updated 13 months ago by James W. MacDonald51k
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Comment: C: Ensembl 93 is out!
... Thank you . Dear Amonida, I'm using Biomart package after fferential expression analysis with DESeq2 package. I use ENSEMBL ID. After differential analysis I would like to obtain the HGNC symbol or VGNC symbol from ENSEMBL ID. The following function work for HGNC symbol but I failed to retrieve vg ...
written 13 months ago by cagenet3420
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...   I also done PCA with DESEQ2 and found nearly 92% for PC1 which is very strange for me...my first axis correspond to genotype and the second one to condition. In fact, I've done all the exploraty analysis and think it was ok but maybe it's not ...       ...
written 3.1 years ago by cagenet3420
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... Yes I did. Here the results for me it's fine ....:  I use ade4 package dds2<-as.data.frame((counts(dds1,norm=FALSE))) lmat<-log(1+dds2) library(ade4) lmatc<-bicenter.wt(lmat) lmatc.pca<-dudi.pca(lmatc,center=F,scale=F,nf=3,scannf=F) s.class(lmatc.pca$co,fac=dds1$genotype:dds1\$conditio ...
written 3.1 years ago by cagenet3420
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... ok thanks for your answer. So basically, from your experience, do you will take them into account for pathway analysis  or should I have to discard them ?  ...
written 3.1 years ago by cagenet3420
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... Hi all, Hi, I am using DESeq2 to get differential expression between two genotypes A (sensitive) and B (resistant) and two conditions (virus-infected ; versus control). I’m using the formula given by Mike in DESeq2 vignette "Example 2: two conditions, two genotypes, with an interaction term” which ...
written 3.1 years ago by cagenet3420 • updated 3.1 years ago by Michael Love25k
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... Hi Anand and Michael, To illustrate that I also have some troubles with few genes that have low read-counts but are DE with a high log2FC threshold. Here is my top DE genes for padj <0.01 and |log2FC| >2. See For example Gene G1 : lo2FC= - 22.01 BUT mean condition 1 (BC.mean)= 59.93 and 0 for ...
written 3.1 years ago by cagenet3420

#### Latest awards to cagenet34

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Error in assay colnames when defining DESeqDataSetFromMatrix following R update

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