User: fawazfebin

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fawazfebin40
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Posts by fawazfebin

<prev • 33 results • page 1 of 4 • next >
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Comment: C: removing decimal from ENSEMBL gene ID from deseq2 output
... How would you alter the command if there are two digits after the decimal point, say ENSG00000000460.15 ? I am not able to remove the numbers after the decimal point in such cases using the above command. ...
written 6 days ago by fawazfebin40
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Comment: C: removing decimal from ENSEMBL gene ID from deseq2 output
... How would you alter the command if there are two digits after the decimal point, say ENSG00000000460.15 ? I am not able to remove the numbers after the decimal point in such cases using the above command. ...
written 7 days ago by fawazfebin40
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Answer: A: Drug resistant vs. Drug sensitive data retreival from TCGA
... Hi @Chaimaa I used both of the columns for categorisation. Cases with ' new_tumor_event_indicator' as 'YES' & tumor_status' as 'WITH TUMOR' were grouped as 'resistant'. The sensitive cases would correspond to the absence of new tumor event & tumor free status. R commands are available to s ...
written 11 days ago by fawazfebin40
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Under the 'Clinical' files you can find different .txt files which gives you information about the drug used (clinical_drug .txt file) and disease recurrence ( follow_up .txt file). The 'new_tumor_event' cases can be grouped as 'resistant' and the cases without a 'new_tumor_event' and that are 'tumo ...
written 19 days ago by fawazfebin40
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'NA's under Gene Names & Gene Symbols : Differential expression Analysis of TCGA data using edgeR
... Hi I was performing a differential expression analysis on TCGA RNA-seq data using edgeR. The results of differential expression analysis has NAs under Gene names and Gene symbols. The EntrezID corresponding to it doesnt not give a valid Gene name. What could be wrong? The following command was ru ...
gene tcga differential expression edger written 6 weeks ago by fawazfebin40
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Sure. Please excuse me for the inconvenience caused. ...
written 3 months ago by fawazfebin40
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... I didnt want to remove the samples, but needed an expert opinion! Great thanks for your time, Kevin. Is there any command to fetch raw HTseq counts from TCGA corresponding to a considerable number of patient barcodes? ...
written 3 months ago by fawazfebin40
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Can you please guide me on the interpretation of the newly created biplot? I wasn't able to label the cases in the plot as well. Thanks! ...
written 3 months ago by fawazfebin40
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Sorry, it was the raw count matrix which was given as input. I am attaching the sreeplot and biplot of PCA which was done on log CPM expression values. > matrix_5FU <- read.delim('5FU.csv',sep = ',',header = TRUE) > Group <- c(1,1,1,1,1,1,1,2,2,2,2,2,2) > gns5FU ...
written 3 months ago by fawazfebin40 • updated 3 months ago by genomax80k
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... PCA was conducted on the raw counts matrix(matrix_5FU) with 14 different cases. > p.5FU <- pca(matrix_5FU[,2:14], removeVar = 0.1) -- removing the lower 10% of variables based on variance > screeplot(p.5FU) Warning messages: 1: Removed 2 rows containing missing values (geom_path). 2: ...
written 3 months ago by fawazfebin40

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Popular Question 7 months ago, created a question with more than 1,000 views. For Access of triple negative breast cancer datasets from GDC
Popular Question 7 months ago, created a question with more than 1,000 views. For Access of triple negative breast cancer datasets from GDC

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