Entering edit mode
3.2 years ago
Nai
▴
50
I have two separate matrix for normal and control. DeSeq2fromHTSeqcount , may i have to run separately for each matrix. I want to create GE.txt for further analysis. Please help me to input the data in Deseq2. In manual as it is saying treated...I did not get that point. list.files means I have mention each sample count file. Kindly explain it?
Hi, can you try this very simple [but effective] advice: How to input data for DESeq2 from individual HTSeq count?
Dear Kevin,
Thankyou. I have normal and cancer samples each folder has 100 - 100 patients which are having same ids. I want to calculate gene expression (i) Using matrix
Eg. Normal folder
Cancer folder
May I to keep in same folder and In
conditions <- (¨normal¨, ¨cancer¨)
. May I have to do like this for matrix.(ii)I want to do with each sample patient which are not technical replicate in one folder.
Eg. Normal folder
Cancer folder
May I to keep in same folder and how I have to manager conditions
<- ()
. What I have to do with sample data.Hi, you probably need to column-bind (bind by column) the files
all.sam.normal.count.mat-tsv
andall.sam.cancer. count.mat.tsv
.In your BASH (shell) terminal, can you show the output of:
?
You need to get your data in this format:
Expression data:
Metadata:
all belong to normal.
Perfect - you need to bind (by column) this data to the tumour data. When doing this, please verify that both datasets are aligned by
Gene Id
. Later, you should import [to DESeq2] the column-bound ('merged') data.I have no idea how to merge the columns. They have same column names. How can I align as GeneId.
I have one folder named Normal and other have cancer which are having same sample number bam files where I executed htseq count separately for each sample in each directory. Simultaneously I executed htseq for all samples in cancer and all samples in normal separately. So I have :
As you showed me. I think I did some thing wrong in HTSeq. Please guide me every step. I will be heartily thankful to you.
I think that you could enlist some help locally, if possible. Keep in mind that textual descriptions of files, code, etc., make it difficult for us to assist you. We would basically need that you provide concrete information about file paths, directory names, contents of the files (even in part), etc.
There is very simple but effective advice here, as I mentioned earlier:
If you have two data files, one with Normal and One with Tumor (as implied above), you can do something like the following:
You can use something of the form above to build your matrix even if every sample is in its own file. If these steps don't make sense, I'm not sure how you'll be able to sensibly execute DESeq2 commands, and I would suggest you go back to basics to learn how to read a file into R, check the order or rownames of a matrix or dataframe, and how to combine columns to form a new dataframe. These are very very basic concepts that you should know how to execute.
Dear Kevin and Seidel
Thank you, Really helpful. I am heartily thankful to you. I try and consult with you.
Can you please stop using the answer field for comments. I moved multiple of these already. Use
ADD REPLY
to keep the thread logically organized.I need your help to design metadata for deseq2. How can I prepare the metdatafile.
Here I don,t have any column name. I am not getting about the following:
Here sample Table = count matrix.tsv directory= ?? design = ??? ( I have 50 samples from cancer and 50 sample from Normal). I am new in R. Kindly help me to mention data in DesSeq2
0
I got an error .
Hi, what is the output of:
Dear Kevin, Now list.files(directory) showing file names. still I am getting same error
My file are eg: N1.bam.count......so on
Also, in your code above, you're leaving out quotes when you supply strings as arguments, e.g. file="myfile.csv", and sep="\t", these are important. Follow the examples very carefully. Experiment with simple steps to get basic things to work. Like, can you read a simple text file in your current directory? (this requires that you (1) know how to create a file, (2) know how to find and specify your current directory, (3) use R to read in a file. If you can do this, you should be able to correctly get DESeq2 to read a file. Read the manual very carefully.
Now I am not getting accurately. what to do.