User: amoltej

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amoltej10
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Australia
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4 months, 1 week ago
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3 years, 1 month ago
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Posts by amoltej

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Problem with WGCNA - Module-trait relationship
... I am using this code for third step - https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-03-relateModsToExt.pdf Yes, I am using complete observations to calculate correlations. There are no NA's in the input dataset for these commands. you can check inp ...
written 4 months ago by amoltej10
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Comment: C: Problem with WGCNA - Module-trait relationship
... Hi Lluis,  Thanks for the reply but the result is still same. I suspect for some reason correlation is not calculating or calculating it to 0 for all the values ...
written 4 months ago by amoltej10
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Problem with WGCNA - Module-trait relationship
... Hello everyone,  I am trying to run the WGCNA on my data set of 87 samples.  First 2 steps executed successfully. In the third step when running following commands I am getting all the "NA"s in the output. moduleTraitCor = cor(MEs, datTraits, use = "p") moduleTraitPvalue = corPvalueStudent(modul ...
wgcna written 4 months ago by amoltej10 • updated 4 months ago by Lluís R310
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SVA behaving weirdly, system is computationally singular , problem with method leek only
... I am running SVA on my data to remove the batch effect from the data that I got from NCBI and data I sequenced.  I am running following command -  > svobj = sva(raw.data,mod,mod0,n.sv=n.sv) Number of significant surrogate variables is:  3  Iteration (out of 5 ):1   Error in solve.default(t(mod ...
sva combat sva leek written 8 months ago by amoltej10 • updated 8 months ago by Jeff Leek490
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is it possible to before and after batch effect removal from the data and see that batch effect removal actually worked
... Hello everyone,  I am using SVA for batch effect removal. I would like to know if it is possible to find out that batch effect removal procedure has actually worked and now there is no batch effect? or simply to visualize data before and after batch effect removal and see how data has transformed? ...
batch effect combat sva comba written 14 months ago by amoltej10 • updated 14 months ago by Vegard Nygaard100
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Comment: C: is it necessary to check batch effect in this case? and how to?
... Thanks for the reply Jakub. after merging respective fastq files, and quality control using FastQC and trimmomatic, I am getting only 1-2% reads discarded from each file. can I take these readings as an indication that all the lanes produced good quality reads? Amol  ...
written 14 months ago by amoltej10
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Comment: C: is it necessary to check batch effect in this case? and how to?
... Thanks for the reply Gordon Smyth. Amol ...
written 14 months ago by amoltej10
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is it necessary to check batch effect in this case? and how to?
... Hello everyone, I have a data set generated from 88 samples in a single run using all 8 flow cells. All libraries were mixed together and sequenced on all the flow cells at a time. So Basically I received 8 fastq files corresponding to each sample. I merged all 8 files for each sample and created ...
batcheffect removebatcheffect combat sva svaseq ranseq written 15 months ago by amoltej10 • updated 15 months ago by Jakub30
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Comment: C: Batch effect problem using SVA showing problems
... Hello, Thanx for the reply. May I know reason behind it? and how the big number for the latent factors is wrong?   Thanx ...
written 17 months ago by amoltej10
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Batch effect problem using SVA showing problems
... Hello everyone,  I am working with 88 samples. To remove batch effect from the samples I am trying to use SVA package. But when I am trying to estimate number of latent factors. I can see in the tutorial and other questions on different forums,  the number of surrogate variables is really small. Bu ...
sva batch effect combat sva written 17 months ago by amoltej10 • updated 17 months ago by Jeff Leek490

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For featureCount - very less Successfully assigned reads

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