User: moradzadeh_k921

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Posts by moradzadeh_k921

<prev • 6 results • page 1 of 1 • next >
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How to get differentially expressed genes in "timecourse" package ?
... hello, I used "timecourse" package for my longitudinal one-sample dataset successfully, But unfortunately I couldn't get differentially expressed genes at the end. Could you please help me to resolve the problem? Many thanks, ...
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How to obtain corrected p-value in BETR?
... Hi Dears, In analyzing my time course data with BETR which is incorporated in the MeV software, I could not find any option for p-value correction. Does this tool calculate corrected p-value? I will be thank you if someone answers. ...
betr multiple testing correction written 3.1 years ago by moradzadeh_k9210
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How does limma calculate log-ratio of fold change?
... Hello everybody I faced a problem in analysis of the data set "GSE27274" by limma package. The parameter "Coef" which shows "logFC" calculated by limma  is different from the one I gained manually. I calculated log2 of treatment expression values average divided to control expression values average ...
limma logfoldchange written 3.2 years ago by moradzadeh_k9210 • updated 3.2 years ago by Gordon Smyth38k
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Answer: A: Uderstanding write.fit output without ID_REF
... My problem is resolved. Thank you very much for your kind answer. ...
written 3.2 years ago by moradzadeh_k9210
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Answer: A: Uderstanding write.fit output without ID_REF
... Thank you for your answer, The output table of limma, doesn't contain ID_REF column, By using these commands: >results<- decideTests(fit.cont,lfc = 1) >write.fit(fit.cont, results, "limma results.txt", adjust="BH",F.adjust = "BH") and when I add "row.names=TRUE" to previous command (> ...
written 3.2 years ago by moradzadeh_k9210
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Uderstanding write.fit output without ID_REF
... Hi Dears, I have problem with understanding limma results while it doesn't have any column show rawnames(ID_REF). when I use the argument "row.names = TRUE" I get this error: Error in write.table(tab, file = file, quote = FALSE, row.names = FALSE,  :    formal argument "row.names" matched by multi ...
limma written 3.2 years ago by moradzadeh_k9210

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