User: meeta.mistry

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meeta.mistry20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
5 months, 4 weeks ago
Joined:
3 years, 10 months ago
Email:
m***********@gmail.com

Posts by meeta.mistry

<prev • 27 results • page 1 of 3 • next >
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mogsa on RNA-seq and ATAC-seq data
... Hi, I am trying to use mogsa to analyze ATAC -seq and RNA-seq data on the same samples. In the vignette example, the data matrices are multiple microarray data. If I use ATAC-seq data, what should I use as input? I was thinking a count matrix for a set of consensus peaks across all samples. However ...
mogsa atacseq written 6 months ago by meeta.mistry20 • updated 5 months ago by mengchen180
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Answer: A: ensembldb and pseudogenes mapping to the same Ensembl ID
... Hi Johannes, Thank you for your quick reply! Both of those alternatives are good to know and very helpful since I use this package often for cross-database annotations. Best, Meeta ...
written 11 months ago by meeta.mistry20
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ensembldb and pseudogenes mapping to the same Ensembl ID
... Hello, I encountered a problem when mapping Ensembl genes to Entrez IDs and was wondering if there was a way around this. For a list of Ensembl gene IDs I used the select function to return to me gene symbols and Entrez IDs.  common_genes <- select(EnsDb.Mmusculus.v79, keys=common, co ...
ensembldb written 11 months ago by meeta.mistry20
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Comment: C: ChIPQC failed on chrM
... Hello I get this same error at the start of my run. Was there a solution to this? My sessionInfo is attached below but also I get a message when I load the library, not sure if this has anything to do with it: No methods found in "RSQLite" for requests: dbGetQuery Bam file has 93 contigs Error ...
written 16 months ago by meeta.mistry20
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Comment: C: ChIPQC report missing figures
... Hi Tom, Adding the Tissue and Condition columns appears to have solved the problem. Thanks very much! Best, Meeta ...
written 18 months ago by meeta.mistry20
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ChIPQC report missing figures
... Hi, I am trying to run ChIPQC on my data but for my final report I get blank plots for CrossCoverage and the Signal profile. I don't get any errors when creating the Chip object nor do I get errors when generating the report so it's hard to troubleshoot.  Here is a link to my report using only chr ...
chipqc software error written 18 months ago by meeta.mistry20 • updated 18 months ago by Thomas Carroll400
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Comment: C: limma paired design with continous covariate
... Thanks for the help. My design is setup like the latter with the different patients as separate factor levels.   ...
written 2.5 years ago by meeta.mistry20
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Comment: C: limma paired design with continous covariate
... Ok will do, thanks! ...
written 2.5 years ago by meeta.mistry20
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Answer: A: limma paired design with continous covariate
... I just realized what you meant. Age is already being controlled for within each pair since the samples for treatment and control come from the same individual. Should have seen that, sorry, Thanks! ...
written 2.5 years ago by meeta.mistry20
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Answer: A: limma paired design with continous covariate
... Sorry, that code is incorrect, it shoudl read:   # Setup design matrix age <- pData(data.norm)$Age treat <- pData(data.norm)$Treatment sample <- pData(data.norm)$Patient design <- model.matrix(~ sample + age + treat) # Fit model fit <- lmFit(exprs(data.norm), design) ...
written 2.5 years ago by meeta.mistry20

Latest awards to meeta.mistry

Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 with high dispersions
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Problems getting Bioc 3.1 after upgrade to R_3.2.0

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