User: sandeep.amberkar18

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Posts by sandeep.amberkar18

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Comment: C: DESeq2 nested effect with 5 variables
... Hi Leaodel, I'm sorry I should've been more clear about the exp. setup. The experiment consists of: - 2 Tissues -- Leaf, Crown - 2 Temperatures -- 21, 27 - 2 Time points -- AM, PM - 3 Dev Stages -- DS1, DS2, DS3 and 4 replicates for each. I posted only a subset of the coldata matrix, ...
written 12 weeks ago by sandeep.amberkar1830
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DESeq2 nested effect with 5 variables
... Hello All, I'm dealing with a rather complex RNAseq experiment that follows a nested structure of the tested variables that could be represented like this: SampleName tissue temp time dev_stage rep Sample1 crown 21 am ds1 rep1 Sample2 crown 21 am ds1 rep3 Sample3 crown 21 am ds1 re ...
R deseq2 rna-seq written 12 weeks ago by sandeep.amberkar1830 • updated 12 weeks ago by leaodel110
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Comment: C: Different filters for wheat in biomaRt package and website
... Thanks a lot Emily, I'll try it out! ...
written 8 months ago by sandeep.amberkar1830
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Different filters for wheat in biomaRt package and website
... Hello, I'm looking to download the Wheat TILLING & SNP data from Ensembl from the biomaRt package in Bioconductor. However, I've noticed that the filters available in biomart website are more than what you have in the Bioconductor package. For e.g. plantsDatabase <- useMart(biomart = 'p ...
ensembl biomart getbm written 8 months ago by sandeep.amberkar1830 • updated 8 months ago by Mike Smith1.4k
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Answer: A: How to choose the threshold of co-expression for gene expression networks
... Broadly what is it that you wish to achieve? There is no explanation for choosing a cutoff, be it of correlation or p-value. However for Spearman correlation there have been widely accepted ranges 1. Low correlation = 0.2 ~ 0.4 2. Med correlation = 0.4 ~ 0.6 3. High correlation = 0.7 ~ 0.9 Per ...
written 19 months ago by sandeep.amberkar1830
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Answer: A: Ensembl id to GeneSymbol with biomart
... More often there are many to many relationships between Ensembl ids and HGNC symbols, which is why it is very tedious to obtain exact gene symbols. It is better to use the mapIds function in org.Hs.eg.db to have those relations. I wrote a nifty function to identify these 1:1 mappings. It returns a l ...
written 2.2 years ago by sandeep.amberkar1830

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