## User: meeta.mistry

meeta.mistry20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 months ago
Joined:
3 years, 6 months ago
Email:
m***********@gmail.com

#### Posts by meeta.mistry

<prev • 27 results • page 1 of 3 • next >
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... 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 ...
written 9 weeks ago by meeta.mistry20 • updated 8 weeks ago by mengchen180
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... 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 7 months ago by meeta.mistry20
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... 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 ...
written 7 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 13 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 14 months ago by meeta.mistry20
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... 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 ...
written 14 months ago by meeta.mistry20 • updated 14 months ago by Thomas Carroll390
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... Thanks for the help. My design is setup like the latter with the different patients as separate factor levels.   ...
written 2.2 years ago by meeta.mistry20
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... Ok will do, thanks! ...
written 2.2 years ago by meeta.mistry20
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... 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 2.2 years ago by meeta.mistry20
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... 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 2.2 years ago by meeta.mistry20

#### Latest awards to meeta.mistry

Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 with high dispersions
Popular Question 2.9 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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