User: jarod_v6@libero.it

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Italy
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3 years, 9 months ago
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Posts by jarod_v6@libero.it

<prev • 62 results • page 1 of 7 • next >
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problem on getpromoters on hg38
... I try to use ChIPseeker  I have peaks anntated with hg38.   library("ChIPseeker") library("TxDb.Hsapiens.UCSC.hg38.knownGene") setwd("~/Desktop/RESULTS2rip/") files=list.files("chr_hg38",full.names=T) files txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peakfile=readPeakFile(files[1]) promoter < ...
chipseeker written 7 weeks ago by jarod_v6@libero.it40
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Comment: C: Deseq2 padj value very low
... thanks It was an error on the preparation on DESeqDataSetFromHTSeqCount so they not change that parameter. Thanks s much! ...
written 9 weeks ago by jarod_v6@libero.it40
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Comment: C: Deseq2 padj value very low
... thanks for the help.. the problem that I  have all the data are in that situation...         res<-results(dds) > head(res) log2 fold change (MLE): Intercept Wald test p-value: Intercept DataFrame with 6 rows and 6 columns baseMean log2FoldChange lfcSE stat p ...
written 9 weeks ago by jarod_v6@libero.it40
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Deseq2 padj value very low
... I have perform differential analysis using deseq2.  In the result I have many genes have very low padj. It is possible?   > res[which.min(res$padj),] log2 fold change (MAP): condition Myoepithelioma vs EMC Wald test p-value: condition Myoepithelioma vs EMC DataFrame with 1 row and 11 columns ...
deseq2 written 9 weeks ago by jarod_v6@libero.it40 • updated 9 weeks ago by Michael Love17k
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Comment: C: Sleuth error Error: Duplicate identifiers for rows
... Sorry, Please delete this question   ...
written 3 months ago by jarod_v6@libero.it40
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(Closed) Sleuth error Error: Duplicate identifiers for rows
... I try to use sleuth package but I have this error: more logs/sleuth_run.log There were 24 warnings (use warnings() to see them) reading in kallisto results dropping unused factor levels ...... normalizing est_counts Error: Duplicate identifiers for rows (4, 5), (10, 11), (16, 17), (22, 23), (28, ...
sleuth biconductor written 3 months ago by jarod_v6@libero.it40
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Rippseeker problem with allocate space
... Dear All. I try to make some comparison using RIPSeek I have this error on Centos 7.0 > setwd("~/Desktop/Analisi_ripseek/") > extdata.dir <- "~/Desktop/Analisi_ripseek/mitico" > bamFiles <- list.files(extdata.dir, "accepted_hits.bam$", recursive=TRUE, full.names=TRUE) > ctlIgM & ...
ripseeker ripseek rip written 3 months 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 7 months ago by jarod_v6@libero.it40 • updated 7 months ago by Michael Love17k
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Comment: C: Different results obtained from mroast and camera from Deseq2 counts
... thanks so much! ...
written 9 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 9 months ago by jarod_v6@libero.it40

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