User: meeta.mistry

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meeta.mistry20
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United States
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1 month ago
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3 years ago
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Posts by meeta.mistry

<prev • 26 results • page 1 of 3 • next >
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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 6 weeks 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 6 weeks 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 7 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 8 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 8 months ago by meeta.mistry20 • updated 8 months ago by Thomas Carroll390
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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 21 months ago by meeta.mistry20
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Comment: C: limma paired design with continous covariate
... Ok will do, thanks! ...
written 21 months 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 21 months 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 21 months ago by meeta.mistry20
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limma paired design with continous covariate
... Hello; I have a simple design, but can't seem to find anything on Bioconductor support that addresses the error I am getting. Any help would be much appreciated. I have a paired design as shown below: > pData(data.norm) Treatment Patient Age Gender HD 3.1 control 3 25 F ...
limma paired covariate written 21 months ago by meeta.mistry20 • updated 21 months ago by Steve Lianoglou12k

Latest awards to meeta.mistry

Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 with high dispersions
Popular Question 2.4 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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