User: sharvari gujja

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11 hours ago
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4 years, 4 months ago
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Posts by sharvari gujja

<prev • 20 results • page 1 of 2 • next >
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WGCNA chooseOneHubInEachModule Error
... Dear Peter, Steve, I am writing to seek your help in using 'chooseOneHubInEachModule' function from the WGCNA package. I am trying to generate hierarchical clustering plot on my data matrix with samples from two groups.  https://rdrr.io/cran/WGCNA/man/orderBranchesUsingHubGenes.html However, usi ...
wgcna chooseonehubineachmodule written 8 days ago by sharvari gujja20
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Comment: C: goseq with hypergeometric method
... Hello Gordon, Thank you for the reply. My concern was not getting more enriched GO terms using hypergeometric option and if I was missing any other parameter. Your explanation is helpful. Thanks ...
written 4 months ago by sharvari gujja20
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goseq with hypergeometric method
... I am running GOseq for mouse data using ~800 genes as input and ~8K genes as background lists.  Running GOseq I get the same number of enriched GO terms using Wallenius and hypergeometric methods. "9 enriched primary GO terms found at BH corrected p-value <= 0.05" Can you please suggest how th ...
goseq written 4 months ago by sharvari gujja20 • updated 4 months ago by Gordon Smyth35k
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Answer: A: Error in "getGSEDataTables" in GSEquery package
... Hello, I get the same error, and wondered if you have any suggestions to fix it. Thanks Sharvari ...
written 22 months ago by sharvari gujja20
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Comment: C: edgeR - inconsistent logFC sign
... I got it. For edgeR, a positive logFC indicates that the gene is up regulated in Condition2 compared to Condition1 and vice versa. ...
written 2.5 years ago by sharvari gujja20
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Comment: C: edgeR - inconsistent logFC sign
... Thank you so much for the explanation. This was really helpful! So, a positive logFC indicates that the gene is up regulated in Condition1 compared to Condition2 and vice versa..?   ...
written 2.5 years ago by sharvari gujja20
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Answer: A: edgeR - inconsistent logFC sign
... The point I am trying to make is that the sign for the logFC doesn't seem right.  Another example for C1 vs. R comparison is: Gene1: AVG_C1 : 18274 AVG_R: 2140 logFC is -0.35 Gene2: AVG_C1 : 18791 AVG_R: 22027 logFC is -0.19   For Gene1 , avg C1 > avg R, and logFC sign is negative For ...
written 2.5 years ago by sharvari gujja20
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Comment: C: edgeR - inconsistent logFC sign
... Yes, I am using raw counts from htseq-count.     ...
written 2.5 years ago by sharvari gujja20
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Comment: C: edgeR - inconsistent logFC sign
... The edgeR code has only 2 groups for pairwise comparison. For C1 vs. R comparison, I modify A and B as: A <- c("C1") B <- c("R")   The point I am trying to make is that the sign for the logFC doesn't seem right.  Another example for C1 vs. R comparison is: Gene1: AVG_C1 : 18274 AVG_R: ...
written 2.5 years ago by sharvari gujja20
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edgeR - inconsistent logFC sign
... Hello Gordon,   I am using edgeR to do pairwise comparison for 3 conditions. The avg values for each condition are:   AVG_C1 : 1596 AVG_C2: 1354 AVG_R: 1934   C1 vs. R gives me logFC of -0.333 and C2 vs. R gives me logFC of 0.066   logFC of -0.33 indicates the gene is down regulated in C1 ...
edger written 2.5 years ago by sharvari gujja20

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Popular Question 22 months ago, created a question with more than 1,000 views. For RUVSeq DE analysis for data with replicate samples and 4 conditions

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