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 5 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 5 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 5 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 6 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 6 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 6 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 6 months ago by spawar20

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