User: spawar2

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spawar20
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Posts by spawar2

<prev • 7 results • page 1 of 1 • next >
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Comment: C: P values from Deseq Analysis
... Thanks Dr. Anders, guess thats the issue. Will update on applying DESeq on raw counts. ...
written 12 months ago by spawar20
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Comment: C: P values from Deseq Analysis
... Sure I will check the batch effects within. Thanks. ...
written 12 months ago by spawar20
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Comment: C: P values from Deseq Analysis
... Sure Dr. McCormack, will apply HTSeq, or something similar, to get integer counts and then apply DESeq on integer counts. Thanks. ...
written 12 months ago by spawar20
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Answer: A: P values from Deseq Analysis
... Thanks a lot, I will go back and check for batch effects and GC content.      ...
written 13 months ago by spawar20
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Answer: A: P values from Deseq Analysis
... Thanks Dr. Anders and Dr. Lluís R, your inputs are valuable guess my experiment didn't show any significant differences. I will look up at "Benjamini-Hochberg adjustment" to understand adjusted p values.  One quick question: What do you mean by normalizing samples better? I applied DESeq on RPKM va ...
written 13 months ago by spawar20
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Comment: C: P values from Deseq Analysis
... Hello Lluís R, thanks for your reply.  1. From about 1000 genes, I get max 10 genes with P value less than 0.05, rest of them between 0.1 and 1, so am confused what should be my threshold for calling them significant genes.  2."The p-value indicates the probability to find such values from a given ...
written 13 months ago by spawar20
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P values from Deseq Analysis
... Dear All,   I was trying to analyze my NGS data with DESeq package and have couple of questions with the same. Could you help me in answering these problems. After I apply nbinomTest, I get P values in range of 0-1. And fold changes of greater and lesser than 1.5. Assuming these as up and down- ...
deseq written 13 months ago by spawar20

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