pca commands

Commands in mothur
1

Hello Everyone,
I am runining the pca command:
mothur> pca(shared=/g1/home/sulbha/MothurSimon/combine.filter.phylip.fn.shared,label=0.03)

After sometime I am getting thei error
“Too many iterations in tqli”

Also, is there a way in which we can break the sequences in taxonomic groups and then form pca plot.


Thanks!!!
2

“Too many iterations in tqli”

How many samples and OTUs are in your shared file?

Also, is there a way in which we can break the sequences in taxonomic groups and then form pca plot.

You can get specific lineages with the get.lineage command.

3
4

How many samples?

5

I have 8107 reads.

Thanks!!

6

8107 Samples or reads? Do you only have 1 sample?

7

I had one water samples which I got sequenced with 16s rRNA primers (V4region) and got more than 100,000 reads, which after filtering I have 8107 reads of one water samples.


Thanks!!!
8

Ok, that’s what I thought. You can’t do PCA or any beta-diversity metrics when you only have one sample. There has to be something to compare it to.

9

Ok, but to this data I mixed some other data from previous study and trying to compare the two, and when I was doing pca I was getting this error.

Also, after getting the lineage can’t we plot pca to see where the groups are formed.


Thanks!!!
10

You have to have more than 2 samples to do pca, otherwise it doesn’t make any sense.

11

Hi Pat,
Can I do pca analysis by combining my samples with few other samples. I want to compare my samples with others, mine is from ice, I want to compare it with soil and other environments.


Thanks!!!
12

Right, but then you’ll have to break those up to make a shared file where you have multiple samples per cutoff.

13

Hi,
For the make.shared file we need a list file.
For this we can combine all the samples fasta file and make one list file. Each sequence in the sample fasta will have name of that particular group. Is that a correct way?


Thanks!!!
14

Hi Pat,
how can I do this?

Thanks!!!

15

I too am getting the error “Too many iterations in tqli” when trying to use the PCA command.

I have 4 samples and there are a total of 103 OTUs in my *unique.an.shared file.

Any thoughts on what the problem could be?

Thanks.

16

Could you send your shared and logfile to mothur.bugs@gmail.com?