User: amyfm

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amyfm0
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Posts by amyfm

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Adding information to the DESeq2 output file (gene name and expression levels fo
... Hi, I can't get the information I want (gene names on my excel output) as I get some error messages: Error in .testForValidKeys(x, keys, keytype, fks) :    None of the keys entered are valid keys for 'ENSEMBLTRANS'. Please use the keys method to see a listing of valid arguments.   I am using cows ...
written 23 months ago by amyfm0
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Comment: C: Adding information to the DESeq2 output file (gene name and expression levels fo
... thank you very much for your answer ...
written 2.0 years ago by amyfm0
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Adding information to the DESeq2 output file (gene name and expression levels for each sample(
... Hi,   After doing DESeq2 with RNA seq data, the output I obtain is an excel file with ensembl transcript ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj. I would like to know 2 things: -If you know if there is any code that I can use in order to obtain the gene name or description in ...
deseq2 gene columns output written 2.0 years ago by amyfm0 • updated 2.0 years ago by Michael Love14k
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Comment: C: R package for molecule interactions?
... well actually I have 2 lists with transcript IDs and I want to find interactions between them at all levels: protein-protein interactions, protein-gene interactions,etc ...
written 2.0 years ago by amyfm0
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R package for molecule interactions?
... Hi, I would like to knowif you know about any R package that allows to find interactions between 2 different gene lists. After a google search, I didn't find any.    Thank you   ...
R interactions package function written 2.0 years ago by amyfm0
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Comment: C: goseq code after DESeq2 -NO IDEA!
... Thank you very much! I am not very familiar with creating vectors or data frames but that should be easy to learn. What I don't understand is how I am supposed to write the length of each gene, as I have thousands! However, the annotation of the genome that I am using is available on Ensembl, so I ...
written 2.0 years ago by amyfm0
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Comment: C: goseq code after DESeq2 -NO IDEA!
... I am using the bovine Ensembl 82, I think it is not listed. But how can I supply the length data and category mappings? Which is the code? The help I would like to have if that someone can provide me the code in order to perform the goseq analysis starting from an excel with the DEGs (in ensembl tr ...
written 2.0 years ago by amyfm0
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Comment: C: goseq code after DESeq2 -NO IDEA!
... thank you very much!!! but actually I don't really know how to continue now. As I said I have just started to use R and I don't know how to continue to do the goseq analysis. Could you help me with the code? In my previous analysis I aligned my RNA sequences against the bovine ensembl82 genome ...
written 2.1 years ago by amyfm0
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Comment: C: Impossible to use goseq package - problem with geneLenDataBase
... I don't know what I did but I fixed it! I started to have more problems so I reinstalled everything and now it seems to work. My problem now is how to do the analysis, I have published other post asking about it because I am lost, thank you very much ...
written 2.1 years ago by amyfm0
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goseq code after DESeq2 -NO IDEA!
... Hi, After DESeq2 analysis of my RNAseq data  in order to obtain differentially expressed genes between 2 cell types, I have a csv file with approximatelly 26000 genes, of which around 6000 genes are differentially expressed (padjustedvalue < 0.05). Now I want to use goseq in order to study pathw ...
goseq deseq2 rstudio code written 2.1 years ago by amyfm0 • updated 2.1 years ago by Steve Lianoglou12k

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