User: prabin.dm

gravatar for prabin.dm
prabin.dm160
Reputation:
160
Status:
Trusted
Location:
USA/Amherst/Umass
Last seen:
4 hours ago
Joined:
11 months, 3 weeks ago
Email:
p********@gmail.com

Posts by prabin.dm

<prev • 35 results • page 1 of 4 • next >
0
votes
0
answers
164
views
0
answers
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 22 hours ago by prabin.dm160
1
vote
1
answer
89
views
1
answers
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 14 days ago by prabin.dm160
0
votes
1
answer
101
views
1
answers
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 20 days ago by prabin.dm160
7
votes
2
answers
140
views
2
answers
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 20 days ago by prabin.dm160
0
votes
2
answers
140
views
2
answers
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 20 days ago by prabin.dm160
0
votes
2
answers
140
views
2
answers
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 20 days ago by prabin.dm160
0
votes
1
answer
101
views
1
answers
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 20 days ago by prabin.dm160
2
votes
2
answers
80
views
2
answers
Answer: C: inherited cancer gene
... There are many such panels available and published. [Oncotype Dx][1] is one I can think of, and here is some from [pubmed][2]. [1]: https://www.breastcancer.org/symptoms/testing/types/oncotype_dx [2]: https://www.ncbi.nlm.nih.gov/pubmed/?term=test%20for%20breast%20cancer%20inheritance ...
written 20 days ago by prabin.dm160
1
vote
1
answer
101
views
1
answers
Answer: A: DESeq2 coutoff or LFC
... This is discussed in the paper Love, Genome Biology. 2014 They mention the default approach of DESeq uses a null hypothesis of 0 LFC. In this case, each gene is compared across treatment for this null hypothesis, and considered significantly different if smaller than the FDR. When you use a fold ch ...
written 20 days ago by prabin.dm160
1
vote
0
answers
260
views
0
answers
Comment: C: DESEQ2 Design formula testing cell type across condition
... In the first scenario where you created a new column, you could use `contrast` but in the 2nd scenario you have to use `name` from `resultsNames`. To compare A vs B, I would suggest revel to make A reference. ...
written 21 days ago by prabin.dm160

Latest awards to prabin.dm

Good Answer 17 days 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 19 days ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Teacher 19 days 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 24 days ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Scholar 25 days ago, created an answer that has been accepted. For C: Fail to delete temporary folder
Supporter 12 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 972 users visited in the last hour