User: jarod_v6@libero.it

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Posts by jarod_v6@libero.it

<prev • 55 results • page 1 of 6 • next >
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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 8 weeks ago by jarod_v6@libero.it20 • updated 8 weeks ago by Michael Love14k
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Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... thanks so much! ...
written 4 months ago by jarod_v6@libero.it20
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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 4 months ago by jarod_v6@libero.it20
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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 4 months ago by jarod_v6@libero.it20
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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 4 months ago by jarod_v6@libero.it20 • updated 4 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 4 months ago by jarod_v6@libero.it20
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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 5 months ago by jarod_v6@libero.it20 • updated 5 months ago by Michael Love14k
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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 5 months ago by jarod_v6@libero.it20 • updated 5 months ago by Michael Love14k
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Biomart error on association gene symbols name
... Dear all. I have perform differential expression analysis using  Deseq2 and tximport from rsem data. When I try to map gene symbol I have some symbol are not annotated. This is some  informtion on my code and my version of tools.     library( "biomaRt" ) #ensembl = useMart( "ensembl", dataset ...
biomart deseq2 written 5 months ago by jarod_v6@libero.it20 • updated 5 months ago by James W. MacDonald45k
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Txtimport for kallisto on hg38 v87
... I try to import the kallisto results on R I use ensembl vs87 . On bioconductor I found the version 86. $ cat abundance.tsv |head target_id length eff_length est_counts tpm ENST00000448914.1 13 12 0 0 ENST00000631435.1 12 11 0 0 ENST00000632684.1 12 11 ...
deseq2 ensembl release txtimport written 7 months ago by jarod_v6@libero.it20 • updated 7 months ago by James W. MacDonald45k

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