User: Sushant Pawar

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Posts by Sushant Pawar

<prev • 23 results • page 2 of 3 • next >
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edgeR Code syntax for without replicate
... Hi all , We want only the Gene Expression for the experiment without replicate, So i just want to confirm that is this code is wright or not . I am providing code below. And what should be the dispersion in "exactTest" . Please help me in that.   ============================================== l ...
edger written 4.0 years ago by Sushant Pawar0 • updated 4.0 years ago by Aaron Lun25k
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Comment: C: edgeR for with no Replicate
... Actually  i am new to this field , I have add this to gene. again i am getting some warning . so please help me . ============================= housekeeping=c("REG3A","GP2") > housekeeping=c("REG3A","GP2") > y0=estimateCommonDisp(y1[housekeeping,]) > y$common.dispersion=y0$common.dispe ...
written 4.0 years ago by Sushant Pawar0
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Comment: C: edgeR for with no Replicate
... but what type of Genes we should store in that variable ? ...
written 4.0 years ago by Sushant Pawar0
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Comment: C: edgeR for with no Replicate
... is it should be the vector or single gene name ? . give some example ...
written 4.0 years ago by Sushant Pawar0
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Comment: C: edgeR for with no Replicate
... is it should be the vector or single gene name . give some example   ...
written 4.0 years ago by Sushant Pawar0
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edgeR for with no Replicate
... Hi all, (edgeR Page no. 21,22 User Guide) I am running program of edgeR for without replicate . I am getting one one error so please help me in that . ==================================== > bcv=0.2 > library(edgeR) > counts=matrix(rnbinom(40,size=1/bcv^2,mu=10),20,2) > y=DGEList(cou ...
edger without replicate written 4.0 years ago by Sushant Pawar0 • updated 4.0 years ago by Yunshun Chen540
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edgeR for without Replicate
... Hi all, Please provide me the commands of "edgeR" for differential express analysis without Replicate. ...
edger without replicate written 4.0 years ago by Sushant Pawar0 • updated 4.0 years ago by Aaron Lun25k
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Answer: A: Replicate for DESeq2
... I have used this syntax for without Replicate by changing only sampleCondition command in DESeq2 . so, is it all wright  ========================================================== library(DESeq2) directory<-"/home/dgl/110_AmpliseqRNA/all_samples_with-replicates/1790_Cervical-Liver_with_LN_R2" s ...
written 4.0 years ago by Sushant Pawar0
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Answer: A: Replicate for DESeq2
... Thank you guys , This is really helpful for me. ...
written 4.0 years ago by Sushant Pawar0
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Replicate for DESeq2
... Hi all , I am running DESeq2 for Transcriptome analysis , Sometimes it is not possible to make replicate for each sample because it increases cost of analysis .So is it all right to simulate the replicate for case and control samples. for e.g - untreated (original counts of control)               ...
deseq2 written 4.0 years ago by Sushant Pawar0

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