User: Bioinformatics

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Posts by Bioinformatics

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Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald gene ontology means you can find various information from any given gene. Look at http://www.geneontology.org    ...
written 9 days ago by Bioinformatics30
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Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald basically I am trying to do gene onthology. there are 100 packages but I prefer to retrieve data from UniProt or ensemble.  ...
written 9 days ago by Bioinformatics30
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Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald   I just made the parsing smaller in order to show I have tried a lot but I cannot figure out what the problem is. For example  hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id', +                                    'ensembl_peptide_id','ensembl_e ...
written 9 days ago by Bioinformatics30
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how to retrieve all attributes from biomart ?
... Basically I want to extract all attributes for several genes ,  when I use the following as example, I get an error , would anyone know why? hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','ensembl_peptide_id','ensembl_exon_id', +                                     ...
biomart written 9 days ago by Bioinformatics30 • updated 9 days ago by James W. MacDonald48k
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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 5 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 6 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 6 months ago by Bioinformatics30 • updated 6 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 9 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 9 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 9 months ago by Bioinformatics30

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