Thanks again for previous help! One question I'm having issue with. I used legacy data, so the GDCprepare function did not work for my query. I was able to design a workaround where I created a count matrix manually, with the metadata in a separate table. How would I go about assigning training labels to data that's not in SummarizedExperiment format? I.e. how would I replicated the below code by using two separate data frames - one for expression data and another for metadata: train_label % as.numeric () train_label
Hi, This is absolutely a great video!! Please, I did not understand your explanation in code line 70: about removing "Metastatic". I am doing similar ML project with "TCGA-BLCA" i.e Bladder cancer but not with ANN. my sample group is "Primary Tumor ,Solid Tissue Normal". I was thinking of how to implement code line 70, but, I actually don't get it. could you brief me in line with my Project? regards,
because you might not have "Metastatic" in your data, so check for unique values and eliminate which is not necessary. unique(sedf@colData@listData$sample_type) will give you unique values in the sample, instead of Metastatic, you could remove which ever type you wish to remove.
Hi I'm having a hard time understanding about finding goi. Can you tell me about the theory of finding good nodes (gene of interst) by summing total weight and bias?
It's not really a great example how it can be used, but a higher Weight and bias signifies the gene expression is being considered as part of the data for the classification process. Even a lowly expressed gene can get a high activation value if they are being multiplied with a big number
hi I tried your code especially for PCA visualization but my graph would not show. It says table of extent 0>. How do I solve this? I am totally new in r. Thank you
![How to check the frequencies of gene mutations in TCGA cancer database [R]](/img/1.gif)
Thanks again for previous help! One question I'm having issue with. I used legacy data, so the GDCprepare function did not work for my query. I was able to design a workaround where I created a count matrix manually, with the metadata in a separate table. How would I go about assigning training labels to data that's not in SummarizedExperiment format? I.e. how would I replicated the below code by using two separate data frames - one for expression data and another for metadata:
train_label % as.numeric ()
train_label
please let me know if you have any guidance!
Great presentation!
Much appreciated!👍
great video
Hi, Thank you so much. This is really helpful
Hi there! Awesome video - super cool stuff! I ran the code
dge
Hi,
This is absolutely a great video!!
Please, I did not understand your explanation in code line 70: about removing "Metastatic". I am doing similar ML project with "TCGA-BLCA" i.e Bladder cancer but not with ANN. my sample group is "Primary Tumor ,Solid Tissue Normal". I was thinking of how to implement code line 70, but, I actually don't get it.
could you brief me in line with my Project?
regards,
because you might not have "Metastatic" in your data, so check for unique values and eliminate which is not necessary.
unique(sedf@colData@listData$sample_type) will give you unique values in the sample, instead of Metastatic, you could remove which ever type you wish to remove.
can you share with me your github for this project?
I was wondering if this could be used in case of 16S amplicon sequencing data. Could you please enlighten me?
Yeap, it can, but how useful the outcome is, it going to be strongly dependent on your interpretation
Hi I'm having a hard time understanding about finding goi. Can you tell me about the theory of finding good nodes (gene of interst) by summing total weight and bias?
It's not really a great example how it can be used, but a higher Weight and bias signifies the gene expression is being considered as part of the data for the classification process. Even a lowly expressed gene can get a high activation value if they are being multiplied with a big number
Time series on binomial outcomes!?
Ex.: gene expression comparison by death versus survival over 30 days!?
🤔
you did not tel me how to select project id because manifest file downloading is tricky you firs need to tel that
hi I tried your code especially for PCA visualization but my graph would not show. It says table of extent 0>. How do I solve this? I am totally new in r. Thank you
Hmm, can you show me what's the code that you run when you get the error? And is your input matrix containing all numbers (no alphabet)?
I am facing the same issue....what can be done?
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
this is the error for PCA