User: spr

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spr0
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Posts by spr

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SomaticSignatures package: how can I get probability of certain mutation type within a signature?
... Hello, I am using SomaticSignatures to extract mutational signatures from my .maf files and in the signature plot, I have noticed that the y axis does not represent probability of mutation type within this particular signature, as the upper limit is well above 1. It rather represents "contribution" ...
somaticsignatures written 8 days ago by spr0
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BiSeq: Read in Relative Methylation data from CCLE
... Hi all,  I would like to perform differential methylation analysis on CCLE RRBS data, however available data have already been processed and are provided as %methylation for CpG clusters. Is there a way to read them in and use BiSeq for differential methylation analysis? Many thanks! ...
biseq ccle written 4 months ago by spr0
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Comment: C: Multiple comparisons with DESeq2
... As far as the multiple comparisons go, even if I specify three levels to be compared with Normal, I still get a single column of LFC values.  Is there a way that I can get three columns, one per each level compared to Normal?  Interestingly, too, the LFC values seem "flipped", as if I specified th ...
written 5 months ago by spr0
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Comment: C: Multiple comparisons with DESeq2
... Thanks so much! ...
written 5 months ago by spr0
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Multiple comparisons with DESeq2
... Hello,  I have a dataset that consists of four conditions (one control, and three different stages of disease) and four batches.  I accounted for batch effects, by:  dds <- DESeqDataSetFromTximport(txi.rsem, sampleTable, ~batch + condition) I then explicitly set the levels of factor condition ...
deseq2 written 5 months ago by spr0 • updated 5 months ago by Michael Love20k
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Comment: C: Package SomaticCancerAlterations, import own .maf file?
... Hi Julian,  I want to use SomaticSignatures on a maf file and I am dealing with the same issue. I loaded SomaticCancerAlterations and tried converting to a GRanges object, however I bumped into this error message:  all.gr <- SomaticCancerAlterations:::.maf2gr("all.maf") Error in maf$Chromosome ...
written 13 months ago by spr0
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Comment: C: Error in tximport, unused argument (reader = read_tsv)
... It seems like reader argument has been replaced with importer. This works just fine: txi.rsem <- tximport(files, type = "rsem", importer = read_tsv) ...
written 14 months ago by spr0
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Error in tximport, unused argument (reader = read_tsv)
... Hello, I tried to re-run the same script on the same samples and I encountered this error.  txi.rsem <- tximport(files, type = "rsem", reader = read_tsv) Error in tximport(files, type = "rsem", reader = read_tsv) : unused argument (reader = read_tsv) The only thing that changed between t ...
deseq2 tximport written 14 months ago by spr0 • updated 14 months ago by Michael Love20k
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Comment: C: Biomart ensembl annotation does not completely match my gene names
... Hi Herve,  I have made some progress, but there are still missing genes. I am using DESeq2 for DE analysis and a tab delimited file a bioinformatician shared with me containing ensembl gene IDs and HUGO symbols. I have since asked them where the file originated from, as I do find discrepancies; ma ...
written 15 months ago by spr0
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Biomart ensembl annotation does not completely match my gene names
... I am using getBM to get start/end positions for my genes, however biomart ensembl hgnz_names only contain 19869 out of my 29581 genes. In my dataset, gene names are HUGO, too. It seems that around 10,000 of my genes are not included in the total of 36,713 genes in biomart ensembl. I checked to see i ...
biomart ensemblbiomart written 15 months ago by spr0 • updated 14 months ago by Hervé Pagès ♦♦ 13k

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