User: cagenet34

gravatar for cagenet34
cagenet3420
Reputation:
20
Status:
New User
Location:
Toulouse, France, INRA
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 4 months ago
Email:
c***********@inra.fr

Posts by cagenet34

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answers
73
views
1
answers
Comment: C: retrieve vgnc gene name or vgnc gene symbol from Biomart after differential anal
... Oups..... ok that means that I need two coffee cups or need holidays....sorry again and thank you so much for your help !!   ...
written 11 weeks ago by cagenet3420
0
votes
1
answers
73
views
1
answers
Comment: C: retrieve vgnc gene name or vgnc gene symbol from Biomart after differential anal
... 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 11 weeks ago by cagenet3420
0
votes
1
answers
98
views
1
answers
Comment: C: tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
... 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 11 weeks ago by cagenet3420
0
votes
1
answer
73
views
1
answer
retrieve vgnc gene name or vgnc gene symbol from Biomart after differential analysis
... 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 ...
biomart getbm mart written 11 weeks ago by cagenet3420 • updated 11 weeks ago by James W. MacDonald48k
0
votes
0
answers
82
views
0
answers
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 11 weeks ago by cagenet3420
0
votes
1
answers
602
views
1
answers
Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
...   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 2.2 years ago by cagenet3420
0
votes
1
answers
602
views
1
answers
Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... 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 2.2 years ago by cagenet3420
0
votes
1
answers
602
views
1
answers
Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... 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 2.2 years ago by cagenet3420
0
votes
1
answer
602
views
1
answer
DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... 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 ...
deseq2 written 2.2 years ago by cagenet3420 • updated 2.2 years ago by Michael Love19k
0
votes
2
answers
2.0k
views
2
answers
Comment: C: too many genes with low read-counts as differential expressed in DESeq2
... 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 2.2 years ago by cagenet3420

Latest awards to cagenet34

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Error in assay colnames when defining DESeqDataSetFromMatrix following R update

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 413 users visited in the last hour