User: aristotele_m

gravatar for aristotele_m
aristotele_m30
Reputation:
30
Status:
New User
Location:
Italy
Last seen:
2 years, 2 months ago
Joined:
4 years, 9 months ago
Email:
a***********@libero.it

Posts by aristotele_m

<prev • 18 results • page 2 of 2 • next >
0
votes
3
answers
5.9k
views
3
answers
Answer: A: Deseq2 supervised heatmap
... Thanks so much for you help! If I use only 10 or 20 genes work really well. I have problem on the visualization plot. I mean  if I use pheatmap I can't see wit the colors all red on the dirst group and all green in the second group. on heatmap.2 gave me the right results. Even if I use this code I ...
written 4.4 years ago by aristotele_m30
0
votes
3
answers
5.9k
views
3
answers
Comment: C: Deseq2 supervised heatmap
... thanks so much, I have one sample design ( treated vs control) . ...
written 4.4 years ago by aristotele_m30
0
votes
3
answers
5.9k
views
3
answers
Deseq2 supervised heatmap
... I want to create a supervised heatmap for the differential expression data obtained from rnaseq analysis using deseq2.   I'm not able to see the up and down genes cluster  expression  even if I plot only differential expresion data results. dds <- DESeq(dds) res<-results(dds) resOrdered &l ...
deseq2 supervised written 4.4 years ago by aristotele_m30
12
votes
2
answers
15k
views
8 follow
2
answers
deseq2 filter the low counts
... Dear all, How can I filter the  counts with low count in Deseq2?  Any suggestion on how to do? dds<-DESEq(dt) count<-counts(dds,normalize=TRUE) filter<-rowsum(count)> 10 thanks so much!! ...
deseq2 lowcount written 4.4 years ago by aristotele_m30 • updated 2.8 years ago by pkachroo10
1
vote
1
answer
1.6k
views
1
answers
Answer: A: How touse SamR
... I resolve I need only to delete 0 on the rows   row_sun<-apply(Dati.coun, 1, function(row) all(row !=0 )) Da<-Dati.coun[row_sun,] ...
written 4.8 years ago by aristotele_m30
1
vote
1
answer
1.6k
views
1
answer
How to use SamR
... Dear All, I want to use samr on my rnaseq data. After  I prepare my normalizate expression value using deseq2 I want to use  samr for detect whihc is the  gene responbile for the difference from on set of data to another. Dati.coun <- counts(dds,normalize=TRUE) colnames(Dati.coun)[match(col ...
rnaseq samr cran written 4.8 years ago by aristotele_m30 • updated 4.8 years ago by Martin Morgan ♦♦ 23k
0
votes
2
answers
529
views
2
answers
Answer: A: Normalizzation indipentent data from RNAAeq experiment
...   These samples are create after subsampling one big RNASeq experiments. I want to be sure the proportion of the expression are the same. So, the simple way is to verify if the  gene I'm studing are remain with the same ratio.     Thanks for the help!! ...
written 4.8 years ago by aristotele_m30
0
votes
2
answers
529
views
2
answers
Normalizzation indipentent data from RNAAeq experiment
... Dear All, I have 5 RNA-Seq experiments  and I want to compare the expression values. I have the raw counts. How can normalize using deseq2? I can't draw any design on this because there is no meaning. What do you suggest ? Thanks in advance for any help   ...
normalization rna written 4.8 years ago by aristotele_m30

Latest awards to aristotele_m

Great Question 2.2 years ago, created a question with more than 5,000 views. For deseq2 filter the low counts
Great Question 2.2 years ago, created a question with more than 5,000 views. For Deseq2 supervised heatmap
Epic Question 2.2 years ago, created a question with more than 10,000 views. For deseq2 filter the low counts
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to use SamR
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Use surrogate variables on DESeq2
Popular Question 3.8 years ago, created a question with more than 1,000 views. For deseq2 filter the low counts
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Deseq2 supervised heatmap

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 351 users visited in the last hour