User: rina

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rina0
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Posts by rina

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variancePartition - testing for individuals
... Hi all! I am analyzing the variance sources of TCGA expression data using variancePartition. I want to check among others the effect of individuals in the variance, but when I specify it at the formula, I get the following errors: > form <- ~ submitter_id > varPart <- fitExtra ...
expression formula variance written 16 hours ago by rina0 • updated 16 hours ago by Martin Morgan ♦♦ 22k
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Comment: C: edgeR. Known cancer genes are not differentially expressed?
... Hi Aaron, Thanks for your comment. The patients groups I am analyzing are grouped together according to their molecular subtypes (that themselves are defined based on expression data), so I would assume that this reduces the variability across the samples. Please correct me if I am wrong. As for y ...
written 5 weeks ago by rina0
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edgeR. Known cancer genes are not differentially expressed?
... Dear experts! I am performing an EdgeR analysis in TCGA samples. I have a subset of the 83 patients I want to check their differential expression in comparison to the 41 samples of normal tissue. Checking for the differential expression of known critical genes (basically almost all the genes taking ...
edger tcga written 6 weeks ago by rina0 • updated 6 weeks ago by Aaron Lun22k
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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 3 months ago by rina0 • updated 3 months ago by Gordon Smyth36k
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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 5 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 5 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 5 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 5 months ago by rina0 • updated 5 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 5 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 5 months ago by rina0

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