User: prabin.dm

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prabin.dm170
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USA/Amherst/Umass
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Posts by prabin.dm

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Correlation vs differential expression testing
... Thank you. I have 3-4 replicates for each gene, so I hope I am excluding batch effects. And similarity in gene expression profile is what I intended to show. ...
written 6 weeks ago by prabin.dm170
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Comment: C: Correlation vs differential expression testing
... Thats great to know. Thank you. The correlation is very important for our study, as with DGE too I would have gone on to demonstrate the same thing, that 2 samples are have similar expression prolifes and the third one stands out. ...
written 6 weeks ago by prabin.dm170
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Correlation vs differential expression testing
... Hi, I have list of 25 genes for which I have done qPCR across 3 different samples. When I do statistical analysis only few only them are differentially expressed. However, if I do a sample-wise correlation analysis, the gene expression data show clear correlation between 2 samples. My question ...
qpcr written 6 weeks ago by prabin.dm170 • updated 6 weeks ago by mike-zx190
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Comment: C: How to assign matching unique IDs to two datasets so that I can merge them corre
... Both datasets have `Gene.Symbol`. Can't you use that to extract column from other dataset ? My guess is both datasets have differing number of rows per Gene.Symbol, so you may not be exactly able to combine two datasets, but at least you will be able to separate info per gene. ...
written 9 months ago by prabin.dm170
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Answer: A: p53 mutations for NCI60 cell lines
... If you need the mutation information, you can use this database. Create a login and look for your cell line or gene. https://portals.broadinstitute.org/ccle ...
written 9 months ago by prabin.dm170
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Comment: C: DESeq2 coutoff or LFC
... the above example I have cited is the correct way of getting LFC cut off. Please see [Michael Love's response here][1] explanation and see the section "Hypothesis tests with thresholds on effect size" in the [DESeq2 paper][2] Although, the approach you have taken is more common than expected, you ...
written 9 months ago by prabin.dm170
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Answer: A: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
... Using the info @i.sudbery's good eye caught. You should change your filter. To find out which filter to use library(biomaRt) mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL") m_ensembl = useDataset(dataset = "mmusculus_gene_ensembl", mart = mart) h_ensembl = useMart(" ...
written 9 months ago by prabin.dm170
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Answer: A: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
... This should also get you the gene symbols [edit] provided you had valid `keys` e.g. ensembl gene ID here. library(org.Mm.eg.db) mapIds(org.Mm.eg.db, data, keytype="ENSEMBL", column="SYMBOL", multiVals = "first") ...
written 9 months ago by prabin.dm170
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Comment: C: convering mouse emsembl gene IDs to Gene names by bioMart and gconvert with no
... Can you post what error you are getting ? also `head(mouse_gene_ids)` output. ...
written 9 months ago by prabin.dm170
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Comment: C: DESeq2 coutoff or LFC
... To obtain meaningful comparison at specific LFC, you have to use `lfcThreshold` and `altHypothesis` in the `result`. Example `resGA <- results(dds, lfcThreshold=.5, altHypothesis="greaterAbs")` . It might be useful if you added your codes to for us to see. ...
written 10 months ago by prabin.dm170

Latest awards to prabin.dm

Popular Question 3 months ago, created a question with more than 1,000 views. For STAR alignment error: ERROR in input reads
Popular Question 7 months ago, created a question with more than 1,000 views. For STAR alignment error: ERROR in input reads
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
Scholar 9 months ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
Scholar 10 months ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Scholar 10 months ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Supporter 12 months ago, voted at least 25 times.

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