User: rina

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rina0
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Posts by rina

<prev • 9 results • page 1 of 1 • next >
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EdgeR between unequal group sizes?
... Hi all I am using TCGA data in order to find differentially expressed genes. The cohort I am using has just 41 normal samples, while the tumor subtypes I am working with have measurements ranging from 80 to 140 samples. Is EdgeR (or any other equivalent package) an option or I cannot get significan ...
rnaseq edger differential gene expression written 6 weeks ago by rina0 • updated 6 weeks ago by Gordon Smyth35k
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Comment: C: Gaia not returning results - load_cnv problem
... This didn't seem to work either. I get the same error regarding the start and end index. ...
written 3 months ago by rina0
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Comment: C: Gaia not returning results - load_cnv problem
... So this error suggests that there is a problem with the markers themselves and not the structure of one of the two matrices?Segment data and markers are both mapped on hg38, so theoretically they should be consistent, right? Is there something specific that I could upload here so you could get an ov ...
written 3 months ago by rina0
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Comment: C: Gaia not returning results - load_cnv problem
... Hi Thanks a lot for your help. I had considered that, but for some reason whenever I change the order ( by: setcolorder(cnvMatrix, c("Sample.Name","Chromosome", "Start", "End", "Num.of.Markers","Aberration"))  I get this error  > cnv_obj <- load_cnv(cnvMatrix, markers_obj, nbsamples) Loadin ...
written 3 months ago by rina0
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Gaia not returning results - load_cnv problem
... Hello, I perform CNV analysis using TCGA data and the gaia package. I have followed the reference manual of gaia, compared thoroughly the format of my inputs, but I still do not get any results back. The run_gaia function runs without any problem, but it always returns an empty data frame. Here ar ...
gaia cnv written 3 months ago by rina0 • updated 3 months ago by Sandro Morganella30
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Comment: C: Adding gene names (or symbols) in my DESeq result
... Not an expert, but I had the same question recently and I did it through >library(fuzzyjoin) >regex_left_join(dataframe, genelist,by=c("IDcol"="transID")) where IDcol is the column containing your IDs in your data frame and transID, the IDs column in your list. Hope that helps! ...
written 3 months ago by rina0
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Comment: C: BioMart missing IDs
... That was a great and really helpful answer! I will take your pointers into consideration and try to tweak the workflow in a way that I avoid converting IDs. Much appreciated!  ...
written 3 months ago by rina0
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BioMart missing IDs
... Looking at the NAs that came up after mapping Ensembl IDs to Entrez IDs using BioMart, I randomly checked one (ENSG00000018607) and it is linked to an Entrez ID that was yet not found. Any ideas what might be the reason? This is the code I used    mart <- useDataset("hsapiens_gene_ensembl", use ...
biomart ensembl entrez gene identifiers written 3 months ago by rina0 • updated 3 months ago by James W. MacDonald48k
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Error: vector memory exhausted (limit reached?)
... Hi everyone! I am new to the bioinformatics world and I would much appreciate your help. I am following the TCGA Workflow tutorial and at the Genomic Analysis part, specifically on the CNV analysis I get this error Error: vector memory exhausted (limit reached?), when trying to load the information ...
gaia tcga cnv mac os x tcgabiolinks written 3 months ago by rina0 • updated 3 months ago by rreck20

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