User: jarod_v6@libero.it

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Posts by jarod_v6@libero.it

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Comment: C: Sleuth error Error: Duplicate identifiers for rows
... Sorry, Please delete this question   ...
written 2 days ago by jarod_v6@libero.it40
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(Closed) Sleuth error Error: Duplicate identifiers for rows
... I try to use sleuth package but I have this error: more logs/sleuth_run.log There were 24 warnings (use warnings() to see them) reading in kallisto results dropping unused factor levels ...... normalizing est_counts Error: Duplicate identifiers for rows (4, 5), (10, 11), (16, 17), (22, 23), (28, ...
sleuth biconductor written 2 days ago by jarod_v6@libero.it40
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Rippseeker problem with allocate space
... Dear All. I try to make some comparison using RIPSeek I have this error on Centos 7.0 > setwd("~/Desktop/Analisi_ripseek/") > extdata.dir <- "~/Desktop/Analisi_ripseek/mitico" > bamFiles <- list.files(extdata.dir, "accepted_hits.bam$", recursive=TRUE, full.names=TRUE) > ctlIgM & ...
ripseeker ripseek rip written 10 days ago by jarod_v6@libero.it40
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Problem on tximport kallisto
... I try to import  data from kallisto using tximport: dds <- DESeqDataSetFromTximport(txi.kallisto, sample_id, ~condition) Error in validObject(.Object) : invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should b ...
tximport written 4 months ago by jarod_v6@libero.it40 • updated 4 months ago by Michael Love15k
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Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... thanks so much! ...
written 6 months ago by jarod_v6@libero.it40
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Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... I have this problem. Camera seem gave one results the mroast gave me  a little different results. You say this is normal. So the problem is what is the right method to choose when you question is to say if there is some enrichment in this list of data? with mroast don't have any significant change w ...
written 6 months ago by jarod_v6@libero.it40
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Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... so if I use tximport$counts I obtain total different results...(if mroast see up as direction then I found down) ...
written 6 months ago by jarod_v6@libero.it40
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Different results obtained from mroast and camera from Deseq2 counts
... I have import data on deseq2 using tximport from rsem results. After create the rlog object I  try to use mroast and camera on  some pathway. This is the script I use: files <- list.files(path=path, pattern="*.ensembl.csv", full.names=T, recursive=FALSE) tipo<-list() result_camera<-data. ...
limma camera mroast tximport written 6 months ago by jarod_v6@libero.it40 • updated 6 months ago by James W. MacDonald45k
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Comment: C: how to apply correctly geneSetTest on deseq2 data results
... thanks so much!! Have you some exmple to gave me ,..because I don't found  any example on deseq2 results   ...
written 7 months ago by jarod_v6@libero.it40
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how to apply correctly geneSetTest on deseq2 data results
... I would like to check if some gene signature are enriched as up-regulated on my rnaseq experiment. I have  2 groups and I calculate the differential expression using Deseq2. I have a folder where I have some signature genes and I don't understand how to use geneSetTest. If i use pvalue I have some ...
limma deseq2 written 7 months ago by jarod_v6@libero.it40 • updated 7 months ago by Michael Love15k

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