User: Bioinformatics

Reputation:
30
Status:
New User
Location:
Last seen:
2 months, 1 week ago
Joined:
1 year, 11 months ago
Email:
m************@gmail.com

Posts by Bioinformatics

<prev • 52 results • page 1 of 6 • next >
0
votes
0
answers
82
views
0
answers
Comment: C: how can I interpret the fold change of Dseq2
... @ta_awwad please read my question carefully  ...
written 9 weeks ago by Bioinformatics30
0
votes
0
answers
82
views
0
answers
how can I interpret the fold change of Dseq2
... I have a question regaridng the conditon  my condition is like below  condition <- factor(c(rep("CondA", 5),rep("ConB", 5))) > condition  [1] CondA CondA CondA CondA CondA ConB  ConB  ConB  ConB  ConB  Levels: ConB CondA​ what can I understand from log2fold change. does it mean that a gene ...
dseq2 written 10 weeks ago by Bioinformatics30
0
votes
1
answers
94
views
1
answers
Comment: C: make a dash instead those gene that do not have ortologue
... @Mike Smith thanks this is difently helpful but in case if the gene names exist and similar in both. do you know what I am trying to do? I am trying to find the orthologue of a mouse gene. is there a possibility to evaluate them based on chromosome or DNA level? how people evaluate the orthologue to ...
written 3 months ago by Bioinformatics30
0
votes
1
answer
94
views
1
answer
make a dash instead those gene that do not have ortologue
... I want to convert a set of genes which I can use the biomart to convert them      musGenes <- c("Hmmr", "Tlx3","STSRAAA1", "Cpeb4")     convertMouseGeneList <- function(x){     require("biomaRt")     human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")     mouse = useMart("ensembl", ...
biomart written 3 months ago by Bioinformatics30 • updated 3 months ago by Mike Smith2.7k
0
votes
1
answer
126
views
1
answer
how to create index
... how can i use Rsubread​ to make the index based on human reference? i could not find the command  In their documentation, I can see the following  ref <- system.file("extdata","reference.fa",package="Rsubread") buildindex(basename="reference_index",reference=ref)​ but I don't know how to build ...
rsubread written 3 months ago by Bioinformatics30 • updated 3 months ago by Mike Smith2.7k
0
votes
1
answers
161
views
1
answers
Comment: C: what happened in limma or Desq2 for ANOVA
... actually one ignores the intercept and one involve the intercept . I am wondering which way is the right way to do ?  ...
written 3 months ago by Bioinformatics30 • updated 3 months ago by Gordon Smyth33k
0
votes
1
answer
161
views
1
answer
what happened in limma or Desq2 for ANOVA
... I know that for limma we use the following for when we have 2 control and 2 treated design <- model.matrix(~c(rep(0,2),rep(1,2))) and for Deseq2 condition <- factor(c("Control","Control","Treated","Treated"))   Now I have this questions one specifically for limma  1- does it matter i ...
limma written 3 months ago by Bioinformatics30 • updated 3 months ago by Gordon Smyth33k
0
votes
1
answers
149
views
1
answers
Comment: C: how to analysis htseq-count
... @Michael Love Do you tihnk that htseq-count is ok for expression analysis? what if I take log2 of htseq-count and then use limma? the problem with your package is that i cannot follow the parts due to the fact that you have created a table inside your package. I am pretty good at R , I just want to ...
written 3 months ago by Bioinformatics30
0
votes
1
answers
149
views
1
answers
Comment: C: how to analysis htseq-count
... @Michael Love Thanks, I have read but still could not use it properly. should I follow from 4.2 Starting from count matrices ? my question is that I have put together the samples and so I have one column with my gene ID and 40 columns of counts (20 conrtol and 20 treated) Can you please tell me from ...
written 3 months ago by Bioinformatics30
1
vote
1
answer
149
views
1
answer
how to analysis htseq-count
... I am trying to analysis 40 samples htseq-count data (20 healthy and 20 diseases) with deseq2 I have read the manual of the package but I have the data ready in my workspace . It is a dataframe of 30000*40  The first 20 columns are my healthy and the second 20 are the diseases  Is there anyone who ...
deseq2 written 3 months ago by Bioinformatics30 • updated 3 months ago by Michael Love17k

Latest awards to Bioinformatics

Popular Question 11 months ago, created a question with more than 1,000 views. For unable to update packages: foreign, Matrix

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 137 users visited in the last hour