User: mahmudornob

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Posts by mahmudornob

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Comment: C: Voom shows error message:
... Thanks for your response. I already counted FPKM and confirmed some interesting DEGs with qPCR. I was trying to avoid galaxy and learning some fastest way for future. But seems like I cannot use any recognized packages. Thanks once again for your prompt response. ...
written 5 months ago by mahmudornob0
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Voom shows error message:
... **Dear all,** Please help. I am having trouble to execute Voom. I have just only two samples without any replication (*Arabidopsis* WT and DKO). I am trying to get DEGs. I have written the script following the available tutorials. Initially, it is okay. But whenever I tried to do Voom, it shows ...
edger limma voom written 5 months ago by mahmudornob0 • updated 5 months ago by Gordon Smyth38k
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Comment: C: Error in summarizeOverlaps
... **Dear J. W. MacDonald,** Thank you so much for your prompt response. I really do appreciate it. As per your suggestion, I added asMates = TRUE and yieldSize=1000000 in my BamFileList like this ( I am posting the text here because my level of R script could be compared with "Kindergarten") bamfi ...
written 5 months ago by mahmudornob0
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Error in summarizeOverlaps
... **Dear Experts,** I am trying to find out DEGs between wild type and double knock out mutant lines of Arabidopsis. Following the available tutorial from the internet, I have written the following R script. Everything works well initially except "summarizeOvelaps" function. After around 30 minutes ...
genomicalignments written 5 months ago by mahmudornob0 • updated 5 months ago by James W. MacDonald51k
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Comment: C: Need expert suggestion about Bioconductor package for microarray data anlaysis
... Thanks for your reply. And sorry for being late to respond to you. I somehow missed it. I fixed the problem. However, I am not using microarray anymore as the price of the microarray is much higher than RNAseq in Korea (I have to compare only two samples) ...
written 5 months ago by mahmudornob0
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Need expert suggestion about Bioconductor package for microarray data anlaysis
... **Dear all,** I am just a beginner of R program. I need to analyze my microarray data. So, I have just started (just 2 days only) to practice with one data set available in GEO called "GSE58231" I have compiled the script following the wiki page "Analyze your own microarray data in R/Bioconductor" ...
affy limma written 8 months ago by mahmudornob0 • updated 8 months ago by Gordon Smyth38k

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