User: saddamhusain77

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Posts by saddamhusain77

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Comment: C: Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... Thank you for helping me on this issue. ...
written 5 weeks ago by saddamhusain770
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Comment: C: Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... ``` > dim(countsgenco) [1] 174318 6 ``` The row names of countgenco is feature_id as you could notice above. Countsgenco is nothing but the counts and ctsgenco is cts; I have just added "genco" acronym. It might be relevant to ask, since I have run the code beyond this point just to see ho ...
written 5 weeks ago by saddamhusain770
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Comment: C: Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... I am sorry to bother you again but the dmDSdata output does'nt look like what is there in the vignettes. It shows just 1 genes. ``` > all(rownames(ctsgenco) %in% txdfgenco$TXNAME) [1] TRUE > txdfgenco <- txdfgenco[match(rownames(ctsgenco),txdfgenco$TXNAME),] > all(rownames(ctsgenco) ...
written 5 weeks ago by saddamhusain770
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Comment: C: Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... Yeah sure. I will consider your advice. Thank you for your time. ...
written 5 weeks ago by saddamhusain770
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Comment: C: Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... The gene symbol and description. Please tell me if I have used the function properly as I am getting following output. ``` > chop1 <-function(x) { + sub("\\|.*","",x) + } > ctsgenco4 <- chop1(ctsgenco) > head(ctsgenco4) [1] "0.630859660016231" "0" "28.3130 ...
written 5 weeks ago by saddamhusain770
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Comment: C: Issue during rnaseqDTU analysis
... Thank you Michael. I have just corrected my post and have added entire code I am using. ...
written 6 weeks ago by saddamhusain770
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Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
... HI, I am analysing differential transcript usage on rna seq data and I am stuck at this point- It seems to me that issue is in the ctsgenco object where a single row contains multiple transcript ids but dont know how to correct it. ``` > filesgenco <- list.files( pattern = ".txt",full.names = ...
dexseq rna-seq drimseq rnaseqdtu written 6 weeks ago by saddamhusain770
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Thanks again kristoffer for all the inputs and the support. I will try with genecode annotation. The issue I find with the annotation files is that no two annotation system replicate the results and I have some worrisome data generated using gencode, ensemble and ucsc gtf files and I found signific ...
written 6 weeks ago by saddamhusain770
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Thank you Kristoffer for the clarification. Well, I uploaded knowngene file from ucsc table browser to the galaxy and then downloaded it some 4-5 months ago, so I don't know whether they have updated it recently. Please forward me the link from where you downloaded the file, I am having hard time fi ...
written 6 weeks ago by saddamhusain770
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... I tried with 1.5.6 and got the same error. ...
written 6 weeks ago by saddamhusain770

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