User: Bioinformatics

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Posts by Bioinformatics

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Dseq2 gives the same results no matter the condition ???
... Hello,  I am trying to understand why Dseq2 gives me the same result if I set my condition differently ? I use Raw count values  First way to do  condition <- factor(c(rep("Normal", 10),rep("Tumor", 11)))​​ dds <- DESeqDataSetFromMatrix(dfm, DataFrame(condition), ~ condition)​ keep <- r ...
dseq2 written 3 months ago by Bioinformatics30
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Comment: C: should I get the logarithm of count values when I use standard method
... @Simon Anders I did not mean to offend you. The problem is that if I use count , then I don't know if it will be normalized insdie the standard calculation or not. I read the vinegette very well but to be honest, I have never seen such an explanation, I even read their paper . That is why I ask here ...
written 4 months ago by Bioinformatics30
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should I get the logarithm of count values when I use standard method
... I have a question which is very important for me.  Basically I am buidling my condition like this  condition <- factor(c(rep("Normal", 10),rep("Tumor", 11)))​ The values are count values and I want to know if I am doing the condition correct and if so, should I take the logarithm 2 myself befo ...
dseq2 written 4 months ago by Bioinformatics30 • updated 4 months ago by Simon Anders3.5k
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Comment: C: how can I interpret the fold change of Dseq2
... @ta_awwad please read my question carefully  ...
written 7 months ago by Bioinformatics30
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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 7 months ago by Bioinformatics30
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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 7 months ago by Bioinformatics30
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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 8 months ago by Bioinformatics30 • updated 8 months ago by Mike Smith2.9k
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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 8 months ago by Bioinformatics30 • updated 8 months ago by Mike Smith2.9k
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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 8 months ago by Bioinformatics30 • updated 8 months ago by Gordon Smyth35k
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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 8 months ago by Bioinformatics30 • updated 8 months ago by Gordon Smyth35k

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