User: Sandip Darji

gravatar for Sandip Darji
Sandip Darji10
Reputation:
10
Status:
New User
Location:
USA/New York/Nathan Kline Institute for Psychiatric Research
Twitter:
wondersandy86
Last seen:
1 month, 3 weeks ago
Joined:
2 years, 9 months ago
Email:
d***************@yahoo.com

Posts by Sandip Darji

<prev • 12 results • page 1 of 2 • next >
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Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
... Hello, I was wondering if there is a bug in the latest "edgeR" package as I get warning message after running estimateDisp function as below. ``` > v <- voom(y.norm, design = design, plot = T) > estDisp <- estimateDisp(y.norm, design, robust = T, weights = v$weights) Error in estimateD ...
edger estimatedisp written 9 weeks ago by Sandip Darji10 • updated 9 weeks ago by Gordon Smyth39k
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Comment: C: Visualising effects of observation/sample weights in differential expression ana
... In case someone is still interested (4.4 years later) in links provided by James, here is the URL for second link https://www.itl.nist.gov/div898/handbook/pmd/section4/pmd432.htm ...
written 4 months ago by Sandip Darji10
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Comment: C: Camera and ROAST
... Thank you so much Aaron for yet again clearing my (and I am sure of many others) doubts. You explanation (in general) is beyond what I can describe in words. I have learnt so much from your posts in my last only a year in the field of Bioinformatics/Genomics. Thanks to Gordon as well who is always p ...
written 13 months ago by Sandip Darji10
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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 20 months ago by Sandip Darji10
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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 20 months ago by Sandip Darji10
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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 20 months ago by Sandip Darji10
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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 20 months ago by Sandip Darji10
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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 2.2 years ago by Sandip Darji10
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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 2.2 years ago by Sandip Darji10
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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 2.2 years ago by Sandip Darji10

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