User: Sam McInturf

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Sam McInturf300
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Posts by Sam McInturf

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Technical and biological replates in BitSeq
... Thank you for the response, I have done the PCA for my samples and they cluster as expected, I guess I was just hoping that I could squeeze a little more out of the data :P ...
written 3.7 years ago by Sam McInturf300
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Technical and biological replates in BitSeq
... Bioconductors, tl;dr:  Does bitseq differeniate between biological and technical variation, if it does, how do I tell BitSeq which files are belong to which biological replicate I am looking to use BitSeq to analyze my single end illumina data.  I have a combinatorial design (3x2x2) where each con ...
rnaseq bitseq written 3.7 years ago by Sam McInturf300 • updated 3.7 years ago by Ryan C. Thompson7.3k
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Comment: C: DEXSeqHTML won't run - warning message: In is.na(x): is.na() applied to non-(lis
... Alejandro, Thank you for your reply.  I am sorry to say that I missed the fact that the HTML report was generated.  Although something still seems to be wrong.   When looking at the report I can see genes with DEU and when I select a gene the only menu that works is the results option.  Any idea? ...
written 3.8 years ago by Sam McInturf300
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DEXSeqHTML won't run - warning message: In is.na(x): is.na() applied to non-(list or vector) or type NULL.
... Hello all, I am working on a simple DEU case for Arabidopsis and have run into an error with DEXSeqHTML.  Everything runs fine until I try and call DEXSeqHTML on my DEXSeqResults object and I get an error of  Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I ...
dexseq written 3.8 years ago by Sam McInturf300
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edgeR complex partial multifactorial design
... Hello everyone, I need to make a design matrix, and I can use the approach outlined in 3.3.1 of the edgeR users guide, but I think that there may be a better way to conduct the analysis. I have 36 samples in a 3x2x2 incomplete factorial design. I have three genotypes (wild type, a single mutant, a ...
edger written 5.4 years ago by Sam McInturf300
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Comment: C: Problems Counting Reads with summarizeOverlaps
... Valerie, Sorry for the lame error, was reading your comments about countOverlaps. I found my problem in that the features data had strand information, while my sequencing was not stranded, so by setting the strand information to "*" in the GRanges object and then reduce(split()) I was able to map ...
written 5.4 years ago by Sam McInturf300
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Comment: C: Problems Counting Reads with summarizeOverlaps
... Valerie and Reema, I am using single end reads. I did as Valerie suggested so <- summarizeOverlaps(tx, reads, mode="Union",type = "any") colSums(assays(so)$counts #185,940 which feels silly, allow for double counts and return fewer counts than prior P.S. thank you for your prompt reply, my e ...
written 5.4 years ago by Sam McInturf300
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genomicRanges/Features reads counted in features and inbetween features is not the total number of counted reads
... Hello everyone, I am having trouble counting RNA seq reads with GenomicRanges and GenomicFeatures. Essentially the problem is I have many reads (10 million mapped) and I only can count 200K in features and 300K between features. So obviously I am doing something wrong. I am working with Arabidopsis ...
genomicranges written 5.4 years ago by Sam McInturf300
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Answer: A: edgeR question
... Hello Audra, First things first, when reporting your session info, use use sessionInfo(), include the ( ). First, what are your tab delim files? is this RNA seq data, or some other form of count data. And most importantly what do you want to do in R. Before trying to do much analysis you may wan ...
written 5.4 years ago by Sam McInturf300
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Problems Counting Reads with summarizeOverlaps
... Hello Bioconductors, I am working on an Arabidopsis RNA seq set, and after executing my count reads script, I get a count table with no reads counted (ie sum(colSums(mat)) = 0). I mapped my reads using Tophat2 (without supplying a gtf/gff file) and used samtools to sort and index my accepted_hit ...
biomart rsamtools written 5.5 years ago by Sam McInturf300 • updated 5.5 years ago by Valerie Obenchain6.7k

Latest awards to Sam McInturf

Popular Question 3.7 years ago, created a question with more than 1,000 views. For ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
Popular Question 3.7 years ago, created a question with more than 1,000 views. For ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values

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