User: Sandip Darji

gravatar for Sandip Darji
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Location:
USA/New York/Nathan Kline Institute for Psychiatric Research
Twitter:
wondersandy86
Last seen:
2 months, 1 week ago
Joined:
1 year, 3 months ago
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d***************@yahoo.com

Posts by Sandip Darji

<prev • 9 results • page 1 of 1 • next >
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Comment: C: What does this error mean? - issue implementing SVA
... I used voom transformation on the data from limma-voom package. You can equally use rld or vst transformations from DESeq2 or simply log transformation on counts.  ...
written 10 weeks ago by Sandip Darji0
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Answer: A: What does this error mean? - issue implementing SVA
... Deer Peter, I appreciate your prompt response and I would like to apologize as I was using untransformed data with sva function in R. As sson as I corrected this, it went smooth. Thank you for your input. Sandip ...
written 11 weeks ago by Sandip Darji0
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Comment: C: What does this error mean? - issue implementing SVA
... Deer Micheal, I appreciate your prompt response. Please accept my apologies as I was using untransformed data with sva function in R. As sson as I corrected this, it went smooth. Thanks. Sandip ...
written 11 weeks ago by Sandip Darji0
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Answer: A: What does this error mean? - issue implementing SVA
... Doesn't anyone have answer to this? It seems like a number of people including myself getting the exact same error but can't find the documented workaround. sva ...
written 11 weeks ago by Sandip Darji0
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Comment: C: remove microarray batch effects using Limma
... That's what I thought. Thanks for clarification and that too so promptly. Sandip ...
written 8 months ago by Sandip Darji0
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Comment: C: remove microarray batch effects using Limma
... Dear Dr. Smyth, As Mike pointed out, here is the NOTE on help page of removeBatchEffect: "This function is not intended to be used prior to linear modelling. For linear modelling, it is better to include the batch factors in the linear model.".  In the example above (Answer to Xie Zhi), which you ...
written 8 months ago by Sandip Darji0
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Comment: C: Can I combine quants from SE and PE reads from replicates of same sample in Salm
... Thanks, again. ...
written 9 months ago by Sandip Darji0
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Comment: C: Can I combine quants from SE and PE reads from replicates of same sample in Salm
... Thank you so much Dr. Love for your prompt response.  I am including "batch" vector (batch 1 for SE reads and batch 2 for PE reads). So to confirm, you can treat quants from biological replicates as if they are normal replicates and it doesn't matter whether they are SE or PE. In other words, you c ...
written 9 months ago by Sandip Darji0
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Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
... Dear Dr. Patro, developers of Salmon and BioC community, I have put great amount of effort to find out answer to this question on internet. Couldn't find it anywhere (bioconductor, biostars, seqanswers, github etc.). I have 3 replicates for each sample and one of the replicates from each sample is ...
salmon tximport limma-voom written 9 months ago by Sandip Darji0 • updated 9 months ago by Michael Love18k

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