User: jarod_v6@libero.it

Reputation:
40
Status:
New User
Location:
Italy
Last seen:
6 months ago
Joined:
5 years, 1 month ago
Email:
j*******@libero.it

Posts by jarod_v6@libero.it

<prev • 67 results • page 2 of 7 • next >
0
votes
0
answers
313
views
0
answers
(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 19 months ago by jarod_v6@libero.it40
0
votes
0
answers
211
views
0
answers
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$", recursive=TRUE, full.names=TRUE) > ctlIgM & ...
ripseeker ripseek rip written 19 months ago by jarod_v6@libero.it40
0
votes
1
answer
254
views
1
answer
Problem on tximport kallisto
... I try to import  data from kallisto using tximport: dds <- DESeqDataSetFromTximport(txi.kallisto, sample_id, ~condition) Error in validObject(.Object) : invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should b ...
tximport written 23 months ago by jarod_v6@libero.it40 • updated 23 months ago by Michael Love25k
0
votes
1
answer
638
views
1
answers
Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... thanks so much! ...
written 2.1 years ago by jarod_v6@libero.it40
0
votes
1
answer
638
views
1
answers
Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... I have this problem. Camera seem gave one results the mroast gave me  a little different results. You say this is normal. So the problem is what is the right method to choose when you question is to say if there is some enrichment in this list of data? with mroast don't have any significant change w ...
written 2.2 years ago by jarod_v6@libero.it40
0
votes
1
answer
638
views
1
answers
Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... so if I use tximport$counts I obtain total different results...(if mroast see up as direction then I found down) ...
written 2.2 years ago by jarod_v6@libero.it40
0
votes
1
answer
638
views
1
answer
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 2.2 years ago by jarod_v6@libero.it40 • updated 2.2 years ago by James W. MacDonald50k
0
votes
1
answer
474
views
1
answers
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 2.2 years ago by jarod_v6@libero.it40
0
votes
1
answer
474
views
1
answer
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 2.2 years ago by jarod_v6@libero.it40 • updated 2.2 years ago by Michael Love25k
0
votes
1
answer
985
views
1
answer
Unsupervised heatmap use tpm or rlog gave different results
... I interested on unsupervised clustering of my samples. I have made differential expression analysis using deseq2 after import data as tximport vignette from rsem. I try to compare two heatmap starting from counting  counts or rlog. I found two different results. Is it normal? norm.counts <- co ...
deseq2 heatmap pheatmap tpm written 2.2 years ago by jarod_v6@libero.it40 • updated 2.2 years ago by Michael Love25k

Latest awards to jarod_v6@libero.it

Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2 filter out my expression gene
Great Question 14 months ago, created a question with more than 5,000 views. For Deseq2 PCA plot customize
Popular Question 14 months ago, created a question with more than 1,000 views. For Problem on annotation of Deseq2 on reportingtools
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Deseq2 unsupervised analysis (heatmap row scaling or none?)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 filter out my expression gene
Popular Question 2.2 years ago, created a question with more than 1,000 views. For txtimportData installation on R version 3.3.0 (2016-05-03)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Pheatmap: how to use breaks for pheatmap
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Deseq2 PCA plot customize
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Deseq2 PCA plot customize

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 105 users visited in the last hour